The Phantom of Atlantis
by Marcus S. Lazarus
Summary: -AU, Part 1 of series- As the expedition settle into Atlantis, Elizabeth Weir finds herself drawn into the mystery of the tale of 'the Phantom of the Ancestors', and begins to realise that her team and the Athosians are not alone inside the city...
1. I Bid You Welcome

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: There's no direct connection between them- indeed, the whole thing's just one of those really freaky coincidences-, but if you go on YouTube regularly, I can highly recommend starg8rocks' Phantom/Atlantis videos, located at http://www(dot)youtube(dot)com(forward slash)watch?v(equals)YNuKjj0yGNU and http://www(dot)youtube(dot)com(forward slash)watch?v(equals)JlbSf3lpRI0; by a remarkable coincidence- and I _assure _you it's nothing more than that; the two of us haven't communicated beyond my comments on the videos themselves- they very accurately capture the mood I intend to create here. Whether I succeed in that goal when writing the story itself… well, that's for you to decide

AN 2: This story begins at the moment that the Atlantis expedition enter the city in the first part of "Rising", but there are significant differences between events as they took place in the series and the events as they occur here. The reasons for these changes will be explained over time, but, at the moment, just read on and see if you can spot what's different from the original episode and work your way up from there…

The Phantom of Atlantis

As Doctor Elizabeth Weir stepped through the Stargate for the first time, there was a momentary rush around her, as though something was rapidly hurrying past her in the opposite direction, and then she found herself stepping out of the 'puddle' of another Stargate, this time located in a vast, elaborate structure like nothing she had ever seen before. The hall before her wasn't the largest room she'd ever been in, but it certainly had a great deal of space to spare for anyone entering via the Stargate, and the steps immediately opposite and to the sides made it clear that this wasn't the full extent of the room she was now in. She could only just make out the doors to either side of her, of course- the room was illuminated well enough, but the doors themselves were overshadowed by the balcony-like structures above them-, but it was enough for her to confirm that there were other rooms around there, and the balconies and stairs ahead of her only served to reinforce that fact.

As Colonel Marshall Sumner barked out orders at the rest of the soldiers who'd come through in the first wave to secure the immediate area- she couldn't help but feel that slightly excessive; what was likely to be dangerous in a city that had been abandoned for over ten thousand years?- Elizabeth took in the rest of her surroundings. A brief glance upwards was all she needed to realise that they were currently standing in the upper part of a tower of some kind, based on the sheer height of the ceiling above her, with what looked like Ancient writing illuminated on several of the pillars and walls around them. For a moment, Elizabeth wondered how the writing could have still been illuminated after the city had been abandoned until now- the immediate area she could interpret as the city reacting to the presence of new arrivals, but nobody had gone near some areas and they were still lit up- but she pushed it aside; it was probably just the Ancient equivalent of leaving the lights on in the kitchen to discourage burglars or something.

While Colonel Sumner continued to issue orders as further soldiers arrived, Elizabeth took advantage of the few moments she'd have before the entire expedition to take in the sights and sounds of the room around her, unable to conceal the awe on her face as she took in the location that was now technically hers.

She had been awed when she first saw the Stargate in action.

She had been impressed when she witnessed General Hammond commanding the _Prometheus_.

But now… to stand here and see the building that may have been the greatest creation of the first race to ever evolve in their galaxy, if not the universe itself…

It was incredible.

"Security teams," Sumner said from off to one side of where she currently stood, "any alien contact?"

"_Negative, sir_," a voice responded over the radio.

"_Team Four negative, colonel_," another voice subsequently added.

As more and more of the expedition members and their equipment continued to come through the Stargate, Elizabeth slowly forced her attention off the awe at their new… home, she supposed was the only term that fit… and turned back to look as the rest of her staff arrived, each of them looking around the city with the same awe that she herself had felt as she saw it for the first time.

After a few further moments of taking in the sights around her, Sumner's voice broke her train of thought.

"That's everyone," he said simply.

As the last of the newly-arrived scientists moved to place their equipment down around the hall, Elizabeth removed the radio from her belt and raised it to her mouth.

"General O'Neill?" she said, smiling slightly as she spoke into the radio. "Atlantis base offers greetings from the Pegasus Galaxy. You may cut power to the 'gate."

Almost as soon as those words were out of her mouth, a bottle of champagne was sent rolling through the Stargate, stopping almost exactly in front of her as the wormhole cut out and vanished. Picking up the bottle, Elizabeth smiled slightly as she studied the label- _Bon Voyage! General Jack O'Neill_-, but swiftly turned to look at the rest of the expedition. Glancing up at where Doctor Rodney McKay stood alone at what looked like the Stargate control room, Elizabeth briefly nodded at him- the man wasn't the most pleasant person she'd ever worked with, but she couldn't deny his talents as a scientist- before she turned to look at the rest of the expedition.

"All right," she said, nodding at the mass of soldiers and scientists before her. "We're here now; everyone spread out and see what you can find."

* * *

Up near the ceiling of the hall, unnoticed by the rest of the Atlantis expedition, around the edge of the tunnel in the ceiling that linked the main room with the shuttle bay above it, a silent figure crouched near a small window on one of the walls, studying the assortment of figures now gathered in the hall below with a wide-eyed gaze of incredulity under the gleaming silver mask that covered most of his face. 

After a moment's silent observation, however, the man's expression softened slightly as he looked at the new arrivals to the city, an almost wistful smile visible at the corner of his mouth. Even as the first arrival- a rather weather-beaten looking man in what the figure would guess to be his early to late forties- ordered his men to secure the surroundings, the figure remained still; he was so high up inside the tower that they would never get into a position that would allow them to discover his presence without him realising what was happening and relocating to another location. The slight smile on his face only became broader as the red-haired woman he'd noted earlier spoke into her radio as the last person walked through the Stargate; he'd worried for a moment that the weather-beaten man was in charge of this thing.

If she was speaking to whoever was on the other side, however, it leant some weight to the idea that _she _was in charge…

Which, the figure had to admit to himself, he greatly preferred to the alternative; she struck him as being a bit more… open… to some of the things he'd encountered in his time here than the first man would had been.

However, that brief moment of contentment failed to last long; almost as soon as the smile had spread across his lips, something else seemed to occur to him as he took in the sheer number of people that now filled the floor below him.

His eyes momentarily widening once again under the mask, the figure stood up as much as his current confined space would allow and walked away, heading deeper into the heart of Atlantis even as the new arrivals began to spread out around the city.

The figure may have remained silent since the Stargate had first activated, but his posture and stance made one thing clear; he had something to do, and he was going to attend to it straight away.

* * *

AN 3: OK then, if anybody wants to guess who that masked man was, feel free, but you'll have to wait a while before you learn anything more definite about him (Although I freely admit that his identity's going to become obvious sooner rather than later)… 


	2. Stranger Than You Dreamt It

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

As Elizabeth dumped her bag in a room that could best be described as an office, located a short distance from what appeared to be the main control room for the city, she was only slightly annoyed when her radio activated; as expedition leader, she should have known she wouldn't be allowed much opportunity to have some time to herself before people started calling her about what they'd found.

"_Doctor Weir_," an excited voice said on the other end of the radio, "_you _have _to come and see this_!"

As she pulled the radio off her belt once again, Elizabeth briefly allowed herself to wonder why she'd agreed to something as demanding as this, before she reminded herself that she'd wanted to learn more about the Ancients and this was the only way to do so; the sheer range of discoveries made so far just helped to reinforce why she'd come this far in the first place.

"I have a lot of things to see," she said, trying to make it clear that she was interested in whatever they'd found even as she walked back towards the control room to attend to more immediate matters. "Just be careful."

As she walked into the control room, she instantly turned her attention to McKay as he studied the console before him uncertainly, clearly puzzled at something that Elizabeth couldn't immediately make out.

"Something wrong, Doctor McKay?" she asked, walking over to stand beside the scientist as he curiously studied the control panel before him.

"I'm not… sure, really," McKay admitted as he turned back to look at her, confusion clear on his face. "I mean… well, look at this," he continued, indicating the console before them. Elizabeth noticed that there were several triangular buttons on the console that each featured what appeared to be constellations, much like those on the DHDs in the Milky Way galaxy, making it relatively easy to deduce what this console was for.

"I have to admit, I don't see the problem," she admitted apologetically as she turned to look at her head scientist. "I mean, it's different from the DHDs that we've seen back home-"

"It's not the appearance that's the issue; it's… well, feel it," McKay said, grabbing her wrist and placing it on the console. For a moment, Elizabeth didn't realise what the problem was, and then her eyes widened as the reason hit her.

"It's… warm?" she said, looking inquiringly at McKay for confirmation that she'd noticed what he wanted her to notice.

"Exactly," McKay confirmed, nodding at her. "From what I know of DHDs, they're generally just the temperature of whatever planet they're on unless they've been in recent use and the crystals have been energised; in other words, since this thing isn't meant to have been used for the last fewmillenia, itshould be as cool as everything else here. Since it's warm, that implies that it was used recently, and since just us dialling _in _wouldn't have required this DHD to do anything…"

"Someone recently used it at _this _end…" Elizabeth whispered, the implications of that fact instantly hitting her.

Somebody had recently used the DHD in Atlantis- used it so recently, in fact, that the naquadah generator that powered the DHD had yet to cool off.

Therefore, somebody had recently been in Atlantis very shortly before they'd arrived.

Therefore, somebody was still _living _in Atlantis, and may have recently left the city expecting to be able to return.

_In other words_, Elizabeth mused to herself as she reflected in more detail on what she'd just discovered, _Atlantis may not be as uninhabited as we thought it was when we came here_.

* * *

AN: I have no idea if the above information about the DHDs generating heat when used is even close to being the case, but since it doesn't actively contradict anything we've learned about DHDs in the show, and I need it for the first clues to be provided to the expedition members that there's more going on they know, just assume it is 

* * *

Before she could ask McKay for any further ideas regarding the possible implications of the DHD being recently active, Elizabeth's radio activated once again, forcing her to focus on more immediate matters.

"_Doctor Weir; Colonel Sumner_," the voice at the other end of the radio said. "_Can you come down and meet me, please? We're three levels down from you_."

"On my way," Elizabeth said briefly, before she put the radio back on her belt and glanced over at McKay. "If you come up with anything about your discovery that could help us work out the why of it, let me know as soon as possible; until then, keep quiet about it to avoid panic."

For a moment McKay looked like he was about to protest, but he nevertheless nodded in quiet understanding.

So far, they had no real evidence that Atlantis might have other inhabitants beyond the fact that the DHD was warmer than the rest of the city; there could have been all kinds of alternative explanations for it being warm that hadn't occurred to either of them yet. If they told Sumner or anyone else about the DHD being active before they'd spent any time trying to find out whether there could be another explanation, they ran the risk of starting off a city-wide panic before they even fully knew the situation they were dealing with.

"See what else you can find out," she said, nodding briefly at her head scientist before she turned towards the stairs leading towards Sumner's current location.

* * *

A few minutes later, she had rendezvoused with Sumner a few levels down from the main control room, the man looking at her with a relatively neutral expression even as he continued to hold on to his gun.

"Only been able to secure a fraction of this place," he said, responding to Elizabeth's first question before she could even ask it, turning to walk away from her even as he beckoned her to follow him with a brief jerk of his head. "It's huge."

"So it might really be the city of Atlantis?" Elizabeth asked, looking curiously at the commander of her military division as she walked along after him, wondering what he wanted to show her.

"I'd say that's a good bet," Sumner replied, without elaborating. For a moment Elizabeth was going to ask him what he meant by that, but then she saw what lay immediately before her and all further questions were driven out of her mind.

"Oh my God…" she said, her eyes wide with awe as she walked towards the sight before her. It was a window that looked out from the tower they were currently in- and it _had _to be a tower; it was too tall to be anything else- to reveal a vast city structure laid out before them. Another tower was immediately visible in front of the window, apparently about as tall as the one they were currently standing it, and an assortment of other buildings were positioned around it, each one of varying height.

What really stood out about the view, however, was the ocean surface just visible far above the peak of even the tallest tower that Elizabeth could currently see, as well as all the water spread out before them.

"We're under water…" she breathed softly, almost unable to believe what she was looking at.

"I'd say we're under several hundred feet of ocean," Sumner confirmed, his tone sounding far more grim than Elizabeth's ashe looked up at where the sunlight was only just visible above their heads. "Can't dial out, this could be a problem…"

Before he could say anything more on that topic, the sound of running feet reached Elizabeth's ears, followed closely by the sound of Rodney McKay's voice.

"Colonel, Dr. Weir!" he began, as he hurried towards them. "You need to hear this; we're underwater, but there's some kind of a force field holding back the wa…"

His voice trailed off as he took in the window before him, his pace slowing as he walked over to stand beside them.

"Boy," he said finally, "that _is_ impressive, isn't it?"

After a moment's silence as the three of them took in the sight before them, McKay spoke up once more.

"Uh…" he said, turning back to look at Elizabeth, gesturing back in the direction he'd just come as he spoke, "Doctor Beckett has, uh, found something you should see."

Taking one last opportunity to take in the sight before her, Elizabeth turned to follow McKay towards whatever Beckett had discovered, Sumner close behind him. After a brief walk through the corridors of the city, the three of them arrived in a large, circular room, with Beckett standing on a platform as he faced the glowing form of a woman, slightly transparent, who was currently talking to him.

"It's a hologram," Beckett said by way of explanation, glancing over at the three new arrivals as they entered the room with a slight smile on his face. "The recording loops; this is my second time through."

"What have we missed?" Sumner asked, raising an inquiring eyebrow as he studied the holographic woman in the centre of the room.

"Not much," Beckett replied briefly, before the group focused their attention back on the hologram before them, just as what appeared to be a vast 'map' of the galaxy appeared above them (Briefly, Elizabeth wondered how the figure could be speaking English when this system had been created thousands of years before the language had developed, but shrugged the thought off soon enough; it wasn't exactly impossible to assume that Ancient technology included some kind of translation program that automatically adapted this system to narrate information in a language that those watching it could understand).

"_In time_," the woman said, drawing Elizabeth's attention back to the image before her, "_a thousand worlds bore the fruit of life in this form. Then one day our people stepped foot on a dark world where a terrible enemy slept. Never before had we encountered beings with powers that rivalled our own_."

Elizabeth definitely didn't like the sound of that; the Ancients were generally seen as the most technologically advanced form of life in the known universe prior to their Ascension. If something existed here that could _equal _them, if not surpass them completely…

Elizabeth wouldn't like to face something that dangerous in a fight, that was for sure.

"_In our over-confidence_," the holographic woman continued, "_we were unprepared and outnumbered. The enemy fed upon defenseless human worlds like a great Scourge until finally only Atlantis remained. This city's great shield was powerful enough to withstand their terrible weapons but here we were besieged for many years in an offer to save the last of our kind we submerged our great city into the ocean. The Atlantis Stargate was the one and only link back to Earth from this Galaxy, and those who remained used it to return to that world that was once home. There the last survivors of Atlantis lived out the remainder of their lives. This city was left to slumber, in the hope that our kind would one day return_."

As Beckett stepped down from the platform, the hologram vanished, leaving the expedition members to look around at each other as they took in what they'd just learned.

"Huh," McKay said after a moment's pause. "So the story of Atlantis is true; a great city that sank in the ocean."

"It just didn't happen on Earth," Beckett added.

"Well," McKay said, nodding thoughtfully as he reflected on the implications of their new discovery, "the ancient Greeks must've heard it from one of the surviving ancients."

"I don't like to think they got their asses kicked," Sumner commented, as he glanced over at Elizabeth, this voicing of her thoughts briefly distracting her from the technician that had just hurried into the room to talk to McKay.

"Let's hear it again from the beginning," Beckett said, moving to stand on the platform once again, watching as the woman appeared before them once again…

"Stop!" McKay yelled, looking sharply up at the doctor. "Turn it off."

As Beckett stepped off the platform, Elizabeth and Sumner turned to look inquiringly at McKay.

"Is there a problem?" Elizabeth asked, looking inquiringly at McKay.

"Well… you _could _say that," McKay said, looking slightly uncertain as he looked at the other people in the room. "My team's been running scans of the city, and so far we've only detected a single Zero Point Module in working condition. It looks like it's got a decent amount of power left in it, from what we can tell, but since we can't detect any more…"

"We've got no way of knowing how long it could sustain us under these conditions, right?" Elizabeth asked, looking at McKay for clarification.

"Exactly," McKay confirmed, nodding briefly at the base's commander as he headed for the door of the room. "I'm heading back to the control room; I might spot something that the rest of the team missed…"

* * *

"So you're saying that the only other ZPMs here are depleted?" Sumner asked, looking critically at McKay after the scientist had revealed his findings to them a few minutes later. "We're almost certainly light-years away from anything else the Ancients built in this galaxy, and the only source of power we have is what's connected to the power drive right now?"

"Hey, I'm as confused about it as you are; maybe they didn't want to risk the city being damaged from the potential explosion if something went wrong with the spares, so they kept them somewhere off-world or something like that," McKay retorted, snapping briefly at the expedition's military leader before he sighed and leant against the wall, holding his head in one hand. "I just wish I knew what I was _missing _here; the numbers just don't _work_…"

Glancing over at Sumner, Elizabeth was relieved to see that she wasn't the only one who didn't know what McKay had meant by that last statement; he was clearly as confused as she was.

"'The numbers don't work'?" she repeated, looking inquiringly at McKay. "What numbers?"

"Well, look at the situation here," McKay explained as he turned to look at her. "The city is meant to be powered by three Zero Point Modules when operating at full capacity; based on what we learnt in the holographic chamber, it would seem that the Ancients left Atlantis just as it was at the time, with the ZPMs remaining 'plugged in'- for lack of a better term- in case they ever wanted to return. Obviously, they never actually _did _return, but the reason is still obvious nevertheless..."

"Obviously," Elizabeth said, waving a hand in a prompting manner as she looked inquiringly at McKay. "So… what?"

"_So_," McKay said, looking critically at Elizabeth as he spoke, "if nobody's been here since the Ancients left, how is it that our teams have found three _depleted_ Zero Point Modules lying around, and one connected up to the main power supply that's still almost at twenty-five percent of its full potential power capacity?"

Elizabeth blinked.

She had to admit, the implications there _definitely _weren't promising…

"You think somebody's been here since the Ancients left the city?" Sumner asked, looking critically at McKay as he spoke.

"I'm sure of it," McKay confirmed, nodding resolutely at Elizabeth as he turned to look at her. "There's no sign that they're here _now_, of course, but if they return…"

Sumner sighed slightly as he turned to look at Elizabeth.

"Doctor Weir," he said, already looking slightly apologetic before he'd even said what he was about to say, "under these circumstances, I feel it would be best to send the majority of the expedition members back to Earth until we can better ascertain the current status of Atlantis. Doctor McKay-"

"Can't do that," McKay said bluntly.

After a moment's stunned silence, Sumner turned to glare pointedly at McKay.

"I believe I just gave you an order, Doctor-" he began.

"An order I would be _glad _to obey, were it not for the fact that we _can't _go back to Earth," McKay interjected.

"What?" Elizabeth said, staring at the scientist in ever-growing confusion. "We have a ZPM-"

"We already tried to dial Earth when we realised we had the power to do so," the technician from the hologram room- Elizabeth vaguely remembered that his name was Peter Grodin; she'd tried to memories the names of the expedition when she'd picked out the teams, but it was hard to recall everyone specifically given the sheer scale of people who'd been assigned to the task- said, dialling the gate as he spoke. "We managed to enter Earth's address into the Stargate easily enough, but when the wormhole actually connected…"

As soon as the eighth chevron had connected, the wormhole activated, only for the traditional 'Kawoosh' of energy to be contained by some kind of… the only term Elizabeth could come up with was 'force field'… over the Stargate, preventing the typical 'explosion' and rendering the 'gate virtually useless.

"It looks like the Iris on the Earth 'gate," Sumner commented, as he studied the Stargate before turning to look at Grodin. "Any ideas what's causing it to turn on?"

"As far as we've been able to determine, it's like… well, it's like someone programmed the DHD to activate that force field in the event of someone attempting to dial Earth or any other address in the Milky Way galaxy; when I tried to dial some of our allies, such as Langara and Hebridia, the shield still came up," Grodin replied, looking apologetically at the Colonel as though he was expecting the man to shoot the messenger. "We tried dialling a couple of the addresses from the Ancient database that are located in this galaxy, and the wormhole connected without the shield being activated, but it always activates when Earth's dialled. I tried shutting it down, but the system seems to be protected by a password of some kind, and, given my limited knowledge of the Ancient language, I thought it best not to try and crack it at the moment; I don't think they would have installed anything too damaging in the event of an incorrect password being entered, but I'm not going to risk it yet."

"Did you try sending a message through to the SGC to ask for some suggestions about shutting the shield down?" Elizabeth asked. As much a she'd tried to recruit the best for this expedition, she still regretted having been unable to recruit Doctor Jackson and Colonel Carter from SG-1; their knowledge of Ancient culture and science would have been a significant asset to have on-hand for a situation like this, but if they could just send a message through the Stargate...

Unfortunately, Grodin swiftly dispelled that hope with a shake of his head. "That was the first thing we thought of, but it didn't seem to work; the shield seems to serve to block our transmissions as well as us ourselves. Not only can we not travel back to Earth, we can't even send them a message to let them know what's going on here."

"Is that the way it's designed?" Sumner asked, looking anxiously at Grodin. Elizabeth couldn't blame him; if they couldn't receive signals through the shield when it was raised, they'd have no way of knowing if the wormhole was from one of their teams or somebody else, which would render them vulnerable to enemy infiltration.

"Fortunately, it just seems to be something else that happens when Earth's dialled," Grodin replied, prompting a slight sigh of relief "We sent a MALP through the Stargate to one of the first planets in the Ancient database and we could receive the signal fine with the shield up or down. It would appear that, as far as we can tell, somebody seemed to want to guarantee that Atlantis wouldn't be able to contact Earth in particular, whether it be as a result of physically going through the Stargate or transmitting a message; maybe they wanted to avoid someone sending a computer virus through or something like that."

"Not meaning to poke any holes in your theories," Doctor Beckett said, raising a hand slightly as he looked around the room at the others, "but if that's the case, how were we able to get here in the first place? I mean, if this wormhole activates whenever Earth's dialled…"

McKay shrugged.

"Best guess, whoever set this thing up had no problem with people coming here _from _Earth because they knew there'd be no danger in that direction; they just wanted to stop people from going from here _to _Earth to prevent… something," he said, raising his hands defensively as Sumner glared at him. "Hey, I'm a _physic_ist, not a _psychiatr_ist; how am I supposed to know why people would do something like this?"

"OK, so going back to Earth isn't an option; maybe we could try relocating the majority of the expedition to somewhere in _this _galaxy?" Elizabeth asked. "If there actually is someone living here, it might at least be worth while seeing if they'd be willing to permit some of us to remain to conduct research; maybe we can find a planet out there that would be willing to provide us with somewhere to stay until we make contact?"

For a moment Sumner simply stared silently at her as she stood before him, until he finally nodded in confirmation.

"Agreed," he said simply, before raising a hand to touch his radio. "Security teams one and two, rendezvous in the gateroom; we'll be going through in a few minutes."

Even as the colonel issued the orders, however, Elizabeth couldn't help but wonder if they were taking the right course of action.

Admittedly, their inability to contact Earth was frustrating to say the least, but the fact remained; whoever had done that had almost certainly had Earth's best interests at heart, if he was willing to go to that much effort to stop someone at this end from accessing it.

The question she most wanted to know the answer to right now was, if someone had rendered the Atlantis Stargate incapable of allowing the user to travel to Earth to try and keep Earth safe, what had they been trying to keep Earth safe _from_…?


	3. As Unchanging As The Sea

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

A few hours later, Elizabeth sat in frustration in the room that had already been unofficially delegated as her office, staring at the information on the screen before her as she tried to piece together the puzzle that Atlantis had already presented to them.

It was ironic, really; she'd agreed to lead the expedition to Atlantis because she'd wanted the chance to find answers to some of the mysteries surrounding the Ancients, and yet, in the end, the greatest mystery they'd encountered so far seemed to have been a contemporary one.

Somehow, since the Ancients had left Atlantis, somebody had started to live there.

That somebody who had made Atlantis their home had somehow known enough about Ancient technology to not only know the importance of ZPMs to keeping the city going, but had actually managed to acquire a new ZPM from somewhere and use it to power the force field that was keeping Atlantis intact at the bottom of the ocean.

That somebody had also, for reasons that Elizabeth could only assume were good ones, rendered it impossible for anyone to so much as send a message to Earth via the Stargate from this end.

And, the most important detail of all, that the someone or someones who'd done all that may or may not still be in Atlantis.

Elizabeth may have signed up to lead this expedition to solve mysteries, but she'd been expecting to tackle mysteries about technology or culture; she certainly hadn't been expecting that there'd be a great need for detective work like this when she'd agreed to go to the Pegasus Galaxy.

It was official; just when you thought that life had thrown you all of the surprises that you were going to encounter, it found another way to surprise you. She'd come all this way expecting to discover a deserted city that hadn't been inhabited for thousands of years, and had discovered that not only was the city apparently not as uninhabited as they'd assumed, but that its inhabitants, whoever they were, had gone to great lengths to prevent Earth from being dialled. According to what McKay's team had discovered, the program that activated the shield when the Stargate dialled a Milky Way address was protected by an as-yet unidentified password, with no hints regarding what that password could be to be found anywhere; whoever had done this had clearly not wanted to make it easy for whoever- or _what­_ever- they were dealing with to get to their galaxy.

On the positive side, Elizabeth was confident that they would eventually find the password; even in a language as complex as Ancient, there were only so many possible combinations that could have been used to serve that purpose.

On the negative side of that argument, there was equally no way of knowing how long it would take them to find the right one to get through the shield. They didn't even know how many letters there were meant to be in the password in question; they would essentially have to devote at least half their science staff at a time just to cracking this code if they wanted it to get back to Earth within the year, and even that was optimistic.

If only they knew who had actually inserted this 'security feature'- Elizabeth couldn't think of it as anything else; clearly somebody had wanted to protect Earth from something in this galaxy- into the Stargate in the first place and had an opportunity to talk to them.

Maybe the person, whoever they were, would be willing to allow the team to access the Milky Way galaxy once they knew they weren't going to threaten humanity or whatever race the shield had been erected to protect...

Despite her confusion, Elizabeth couldn't stop a slight laugh from escaping her lips at that thought.

The day things went _easy _for anyone who travelled through the Stargate was the day that the Goa'uld as a whole decided that it was wrong to conquer other civilisations; it wasn't going to happen.

* * *

Unknown to Elizabeth, the object of her thoughts was currently sitting in a small tunnel that he assumed had originally been intended as a maintenance tunnel of some kind, allowing the Lantean engineers access to some of the harder-to-reach parts of the city in the event of them needing to conduct repairs.

_Doctor Elizabeth Weir_… he reflected silently to himself as he studied her, a soft smile spreading across his lips as he looked at her.

So, he'd been right.

It _was _her.

He hadn't been sure at first- so much about her had changed- but it was indeed her.

If nothing else, it was comforting to know that not _everything _had been altered, even if the essential details weren't the same as what had previously occurred (A fact that he was _particularly_ grateful for; he somehow doubted he'd have had so many interesting experiences if things had proceeded as they had the first time).

Now, all he needed to do was wait a few more moments for the failsafe to kick in- he would have done it instantly, but he'd wanted to give himself time to move into hiding in case he'd underestimated the team again and they found him before he could get to safety-, and then…

He shook his head; there was no point continuing along that particular train of thought until he'd formed a better picture of the new arrivals to his city. He already had a relatively good idea of how she would react to him thanks to past experience, of course, but he still had no way of knowing how much she had been changed by what had occurred.

And as for the rest of the expedition...

He shook his head, scolding himself for his concerns.

He'd learned the hard way that nothing could be predicted; all that he could do was try and make his way through life as best he could and hope that things worked out to be at least not as bad as they had been.

He'd waited this long for someone else to come to Atlantis; a bit more time by himself as he tried to come to a decision wouldn't kill him…

Then the chevrons on the Stargate began to light up and he instantly moved away from his original position, taking the tunnel that would lead him back to his original observation 'window' as he studied the scene playing out before him.

If nothing else, he'd like to see her reaction when the city that would be her home rose above the waves...

* * *

Glancing up as the Stargate activated, Elizabeth was more than slightly surprised to see Colonel Sumner and what looked like just over half of his original team come through the Stargate, closely followed by what looked like dozens of refugees dressed in clothing that reminded Elizabeth of some of the many Middle-age level societies that the SGC had encountered during their early travel to Goa'uld dominated planets.

"Colonel Sumner?" she asked, hurrying down the stairs to look inquiringly at her military commander. "Who are all these people?"

"Refugees," Sumner replied, his tone indicating his reluctance at bringing them back with him. "We ran into the local hostiles; things got ugly, a number of us were abducted on both sides, and..."

He shrugged, trying to appear as though he had no strong opinions either way about the situation. "Well, Lieutenant Ford, among others, made a fairly compelling argument for bringing them back with us."

"I... see," Elizabeth said briefly, before she turned to look at one of the new arrivals, this individual being a tall man who gave off a greater appearance of authority than the rest of the refugees. "I'm Doctor Elizabeth Weir, commander of this facility."

"I am Kanaan," the man responded, inclining his head slightly as he looked at Elizabeth. "I wish to thank you and your people for providing us with sanctuary, Doctor Weir; we-"

Before he could continue, the entire city suddenly seemed to shudder once, as though an earthquake of some sort had just taken place- Elizabeth was briefly thrown to the floor, along with some of the other expedition members around her-, and then it began to shudder, shaking slightly every few second as though it was caught in an earthquake of some sort.

"Doctor McKay?" Elizabeth asked, scrambling rapidly to her feet as she turned to look at the scientist as he stared in shock at the read-outs before him. "What just happened there?"

"I can't- I don't know!" McKay protested, staring in confusion at the read-out on his laptop. "One minute we're all fine, the next the city just... just..."

His voice trailed off as he looked over at the large window at the opposite end of the tower from the Stargate, his eyes widening as he took in the sight before them. Spinning around to see what had attracted his attention, Elizabeth was only just in time to see the water that had previously filled the window was becoming increasingly lighter, the deep blue that had previously filled the window becoming lighter as the shuddering increased.

"Oh my God..." Elizabeth whispered as she hurried over to stare out of the window, barely even registering the presence of Sumner and some of the new arrivals behind her. As she reached the window, the water before her seemed to almost instantly vanish to reveal clear blue skies, the tower now above the water rather than underneath it as it had been upon their arrival. As she stared out of the window in awe, Elizabeth couldn't stop a broad grin from spreading as she saw a brilliant sun shining down onto a clear blue ocean that spread out around them as far as she could see, the water only broken as the shorter buildings in the city rose out of the water around them, the towers rapidly bursting from their watery resting-place like trees growing to full height in a matter of seconds.

It was, without a doubt, the most incredible sight that Elizabeth had ever seen in her life. The vast city of the Ancients rising out of the ocean to greet the air and the daylight once again, the water tumbling off it as it rose ever higher above the waves, the glass and metal shining in the sun to create the illusion of being made of gold rather than whatever materials the Ancients might have used in the construction…

In all her life, as she looked out at the city that was now her home and her command, Elizabeth doubted she would ever witness anything as awe-inspiring as this ever again.

"Well," she said at last as the lights- which had dimmed as the city rose- came to light once again, allowing a slight smile to remain on her face as she looked over at where Sumner and McKay stood off to her right in front of the window, "it would appear that we've already made our mark on this city."

Then her eyes narrowed as she looked at McKay. "And I want answers as to _how _this happened in the first place as soon as possible, is that understood?"

What she'd just seen may have been incredible to witness, but if this city was going to rise off the bottom of the ocean without providing her and her staff with advance warning beforehand, she'd like to know _why _it was doing that in the first place.

* * *

An hour or so later, Elizabeth stood in the control room with Sumner and McKay, looking patiently at McKay even as she took in what Sumner had just told them about their first mission in Pegasus.

Having arrived at the planet they had dialled- the planet in question being Athos, as they now learned-, the team had quickly made contact with the local Athosians, led by a woman called Teyla Emmagan, who had revealed the presence of this galaxy's version of the Goa'uld; the Wraith, powerful aliens who apparently regularly abducted humans from various worlds throughout the galaxy. The Athosians had been unwilling or unable to reveal the Wraith's purpose in doing so, and Sumner had seen no need to pressure them for further information on that front at the time, instead focusing on the more immediate issue of finding out if they would be permitted to send at least some of their people to stay with the Athosians while they attempted to learn more about the current situation on their new planet (It had been decided to avoid mentioning Atlantis at first as there was no telling how the Ancients were perceived in this galaxy; Elizabeth had been on too many diplomatic missions where someone's perceptions of others were affected by where they lived or other matters of origin, so it had been decided to keep the specifics quiet until they could better determine the situation here).

Before negotiations could proceed much further than discussions over dinner and a brief tour of a nearby ruined city, a small group of Wraith ships had attacked Athos, abducting several Athosians, Teyla amongst them, and various members of the military teams, among them Sumner's second-in-command- a Captain Louis Gemmel, Elizabeth recalled; she hadn't had much chance to speak to him so far-, before departing through the Stargate once again. With the village decimated, Lieutenant Ford- who had been stationed at the Stargate and thus been able to note the symbols of the address that the Wraith had dialled to when leaving the planet- had decided that the best thing that could be done for the Athosians was to relocate them to Atlantis, thus protecting them from any future attacks at the hands of the Wraith. Sumner had initially objected to the idea, of course, but when some of his team had pointed out the benefits of the Athosians' knowledge of the Pegasus Galaxy, coupled with the fact that aid in exploring the city couldn't fail to be a good thing, he had finally agreed to the suggestion and allowed the Athosians to accompany them back to Atlantis.

"Well," Elizabeth said as Sumner concluded his report (It was far too factual to be called a 'story'; he hadn't even attempted to embellish the events that he narrated, resulting in it being, quite frankly, one of the dullest reports she'd ever heard even if she'd never admit to it), "I think it's safe to say that we've determined the reason somebody wanted to limit access to Earth."

"Quite," Sumner agreed. "From what I saw of these 'Wraith', their technology appears formidable; an encounter between us and them might be relatively evenly matched these days, but who's to say what state we'd have been in if they'd managed to gain access to Earth before now?"

"Precisely," McKay interjected, nodding in agreement at Sumner as he continued to study his laptop. "Of course, we'd need to get a better idea of the Wraith's current level of technology- to say nothing of what they are personally; parasites like the Goa'uld or something else?- before we can make any real assessment of just how much of a threat they'd be to us; once we've tracked down the planet where those ships took their prisoners, we'll probably have a better idea of what they're capable of..."

"We can focus on that later," Elizabeth interjected, glaring at Rodney in a manner that made it clear there was no room for argument in this case; she was still uncomfortable about the prospect of sending a team on a mission against a primarily unknown enemy when they were still struggling to find their feet. "In the meantime, have you discovered why the city released itself from the ocean floor like that?"

"That's it," McKay replied.

Elizabeth blinked.

"'That's it'?" she repeated, looking incredulously at McKay. "Doctor McKay, you're telling me that you could work out how the Zero Point Modules work, and the best explanation you can come up with for this city rising to the ocean surface after spending the last ten thousand years underwater is 'That's it'?"

"Look, I ran through every possible cause for this that I could think of; _none _of them fit the facts that we have available!" McKay protested, looking indignantly at her. "I found a reference in the code- after my _entire _staff spent the better part of an _hour _combing through it, I might add- to a failsafe release mechanism that's meant to make the city rise above the water if the power falls below a certain level, but even with the demands caused by our presence, with our naquadah generators taking on the demand of some of the more minor systems we should have been able to keep the city operating at a sufficient power level to stay at the bottom of the sea for _weeks_, if not months! There was no _reason _for us to rise up _then_-"

"But we would have risen eventually, correct?" Elizabeth interjected, looking pointedly at McKay as she folded her arms and waited for him to confirm her statement.

"Well…" McKay muttered, evidently trying to think of a better way of saying what he was about to say before he sighed in frustration. "OK, yes, _eventually _we would have risen to the surface anyway…"

"At which point we would have had absolutely no usable ZPMs available to us at all and would not be able to erect the shield to protect us in the event of an attack, correct?" Elizabeth asked. She had only understood the essential basics of the information she'd learned from the research team back at the Antarctic base- she was a diplomat, not a scientist, after all-, but she'd learnt enough to know that the power produced by even one ZPM was greater than several naquadah generators put together.

For a moment, McKay simply stared silently back at Elizabeth, before he sighed and threw up his hands in resignation.

"_Fine_," he groaned in frustration. "I admit it; we _would _have been in trouble if we'd just remained at the bottom of the ocean indefinitely, we would have unnecessarily drained the ZedPM for nothing more than some extra camouflage that we might not have even needed for several months…"

Once again he paused, waving a hand as though he was trying to come up with an appropriate metaphor, before he spoke again. "But that doesn't change the fact that somebody _deliberately _activated that failsafe ahead of schedule!"

"One of your staff-" Sumner began.

"Colonel, nobody intelligent enough to be permitted to join my staff would have been _stupid _enough to try anything that might shut down the force field that was the only thing keeping the ocean from flooding the entire city and _killing _everyone inside it," McKay countered, glaring over at Sumner with a clearly hostile expression at the implication that one of his staff could have made such a mistake. "Besides, this activation has no indications of being caused by something we did to the code; as far as I can tell, someone deliberately _ordered _the city to do this."

As he turned to look at Elizabeth, McKay was momentarily silent as he stared at his expedition leader, clearly wanting her to understand the implications of what he was about to say. "Somebody who sent that signal from a building located all the way over…"

Reaching over to indicate the map of the city on a screen beside him, McKay tapped an area in the upper-right corner of the city…

Specifically, in an area that Elizabeth _knew _she hadn't ordered any teams to search prior to the city rising to the surface; even if somebody had been in that area, nobody would have been foolish enough to touch anything that might have had the potential to do something like this.

She understood the implications of McKay's reasoning well enough; she just wasn't sure she liked them.

"Somebody _else _activated the failsafe?" she asked, looking anxiously at McKay for clarification. "As in, somebody _not _a member of this expedition?"

"Correct," McKay said, nodding at her with a slightly apprehensive expression as though he was afraid she was going to follow ancient tradition and kill the messenger. "I've tried to bring the city's sensors on-line to see if I can track who did it and where they went afterwards, but I'm really not holding out any hope…"

"Once you've got the Stargate address for where the Wraith took our people, get right on it," Sumner said, looking grimly at McKay as he stepped forward, clearly resuming command of the situation now that the immediate question had been answered. Elizabeth stepped forward to voice her objection- they still knew too little about the Wraith to risk an actual assault on them- but Sumner raised a hand to stop her. "Don't try and change my mind, Doctor Weir; this is a purely tactical decision. If these 'Wraith' learn what we're capable of and where we're located, what we've learnt of them suggests it would be unpleasant at best; we cannot take the chance that they will give away vital information if held for too long."

"Colonel Sumner," Elizabeth stated, folding her arms to stare back at her military commander, "while I acknowledge the merits of your argument, I ask you if you have considered the possibility that the Wraiths' prompt arrival at that planet may be as a result of inside information-"

"In other words, one of the Athosians may have informed them?" Sumner replied, shaking his head slightly. "I considered that, Doctor Weir, but even if so, it's unlikely that they'll manage to send a message now if there is a traitor; we can safely monitor them and determine if there is a mole amongst them."

With that said, Sumner allowed himself to relax, and a slight smile crossed his face as he glanced behind Elizabeth. Turning around, Elizabeth couldn't stop a slight smile from crossing her face as she saw two of the Athosian children chasing each other through the main hall around the other expedition members. One of them was wearing a grey twisted face-mask with long white hair that Elizabeth had gathered was meant to represent a Wraith- she wondered if the mask was an accurate depiction of a Wraith or simply based on loose description- while the other boy was wearing a strange silver-coloured mask that covered most of his face.

For some reason, it was the silver mask that most attracted Elizabeth's attention. She wasn't sure why- it wasn't that elaborately-made, and it clearly wasn't even made of real silver-, but something about it made her wonder. Maybe it was the fact that the boy wearing it was actually _chasing _the boy wearing the Wraith mask; it suggested that the mask was intended to represent some heroic

"Besides," Sumner's voice said, breaking into her train of thought, "I think it's safe to say that, even if there is a spy among them, not all of them are like that."

Shaking her head slightly in frustration at her distraction, Elizabeth turned around to face Sumner once again.

"All right," she said, nodding in agreement at her military commander. "Just be certain that you actually have a _plan _once you find where the Wraith have gone."

Even as Sumner and McKay left to study the Ancient database, however, Elizabeth couldn't shake her concern at the implications of McKay's earlier discovery regarding the shield.

Once again, they had discovered evidence that somebody else had been in the city.

The only difference was that, on this occasion, it was evidence that somebody else was in the city with them _now_.

_Where could they be_? Elizabeth wondered as she studied the window behind the Stargate, looking out at the city before her.

_And more importantly… what do they _want?


	4. They Have Returned To You

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Just to clarify, Elizabeth's meeting with Carson regarding the severed Wraith hand took place between this chapter and the last chapter; I saw no point in including it because it's the same as it was originally

The Phantom of Atlantis

A few hours later, as Elizabeth stood in the control room waiting for Colonel Sumner's team to depart, she still found herself unable to fully believe how rapidly everything had gone following her decision to permit the rescue attempt to take place. Thanks to the Ancient database on Stargate addresses- one of the few things in the Atlantis databanks that there was no chance of misunderstanding, thankfully-, McKay had eventually been able to identify the only possible 'gate address for the symbols that Lieutenant Ford had seen activate on the DHD, but the subsequent MALP test had revealed that the Stargate in question was located in orbit around a planet rather than being on the planet itself, thus making it impractical at best to send a conventional team through.

Fortunately (Or unfortunately, depending on your perspective; Elizabeth still wasn't sure how she felt about that particular discovery, particularly after what Carson Beckett had told her about their new enemy following his examination of the severed Wraith arm Sumner's team had recovered from Athos), an earlier search of the city had resulted in the discovery of what could best be described as a 'shuttle bay' located directly above the 'gate room, containing several small space ships that could clearly be piloted through the Stargate. After gathering almost every ATA-gene-positive member of the expedition into the 'shuttlebay' to test what McKay had termed 'Gateships' (On the grounds that they were ships that went through the Stargate; personally, Elizabeth thought the name displayed a significant lack of imagination but had declined to comment on the grounds that she was unable to come up with something better herself), Sumner had selected a pilot for the mission in the form of Air Force officer Sergeant Markham, and subsequently gathered his assault team together.

At the moment the staff were making the last few checks of the few Ancient systems whose purpose they'd been able to determine inside the control room, while Sumner's selected 'strike force' of about ten assorted marines and soldiers gathered into the 'Gateship'. With nothing immediately requiring her specific attention following Carson's examination, Elizabeth had decided to make sure things were prepared in the control room, and just hope for the best when it came to Sumner and his team once they were through the Stargate.

"Are we ready here?" she asked, looking over at McKay as he studied one of the control panels.

"I have _no _idea," the scientist groaned, placing something down on the console as he walked around it to join her. "This technology is so far beyond us; I haven't clue what we're dealing with. For all I know, we could…"

As Elizabeth turned to glare at him, not in the mood for further complications at a time like this, McKay simply sighed. "Yeah, we're ready."

With that said, he walked over to stand in front of the DHD, his hands on either side of the console as he waited for the confirmation call from the hanger.

"_Flight_," Colonel Sumner's voice finally said, "_this is Gateship One; all systems are go_."

"Affirmative, Gateship One; you are clear to launch," McKay replied, moments before the Stargate began to activate. As soon as the final chevron had engaged and the wormhole formed, the roof of the main room opened and the ship- Elizabeth couldn't quite bring herself to call it the 'gateship'; it just didn't _feel _right, somehow- lowered itself from the hanger to hover in front of the Stargate, its sleek greenish-grey form reminding Elizabeth of an animal ready to pounce in the brief moment before it entered the Stargate.

After what she'd learned of this latest enemy race from Carson's examination of that hand, as the Stargate shut down automatically, Elizabeth could only hope that this 'animal'- to continue her original metaphor- possessed enough power to do the job.

"Alert me as soon as we hear anything from them," she said, as she glanced back at the technician currently at one of the consoles before she looked back at McKay. "Stay in touch with the expedition teams and let me know the moment you find anything that we might be able to use at the moment to help with our current situation; I'll be in my office."

* * *

After about an hour of sitting and waiting for a report, however, Elizabeth soon came to realise the main disadvantage of being a civilian in this kind of situation; she had to simply wait and find out how things were progressing for her staff.

It was funny, really; she'd been anxious when SG-1 had gone on that mission to try and track down what they'd thought had been Atlantis, but it hadn't been as serious as it was now. Maybe it was because, unlike then, she'd had more of a choice in the matter; with Colonel O'Neill dying from the Ancient knowledge in his mind, they'd had to move fast if they were going to accomplish anything, but here she could have refused to send them on the mission relatively easily.

When Colonel O'Neill's life had been dying from the Ancient knowledge in his head, it had been a choice between doing nothing and losing the chance to find Atlantis, or doing something and taking that chance.

Here, the choice had been do nothing and definitely lose around ten people, or do something and potentially lose twice that number; it really wasn't as clear-cut as it had been during the Anubis incident.

Just because she'd known what she _had _to do in that situation- it would have been an extremely bad idea to leave people in the hands of the enemy, after all- didn't mean that she _liked _having had to do it in the first place…

Sighing, she got up from her new desk and walked down the stairs to stand in front of the Stargate, a reflective expression on her face as she stared at the device that had caused so much change back on Earth over the last seven or eight years, to say nothing of what had taken place in the distant past because of it. So many alliances had been formed… so many people had been lost… so many advances had been gained…

And in the end, no matter how far they came, there was always at least one advanced civilisation out there that saw humanity as nothing more than something to be stepped on.

"Doctor Weir," McKay's excited voice suddenly said from behind her, breaking Elizabeth's train of thought even as she continued to stare reflectively at the Stargate, "we're getting reports in from all over the city; there's some pretty interesting stuff. We've only been able to provide power to certain sections, but even then, the things that are coming up are just…"

As he drew closer to her his voice trailed off, clearly realising that she wasn't paying any attention to what he was saying to her as she continued to stare silently at the Stargate.

"I should never have let them go," Elizabeth said after a moment's silence, acknowledging that Rodney would probably want some explanationf or why she was simply staring at the Stargate like this.

"For what it's worth…" her head scientist said after a moment's pause, "you made the right decision. Give them time."

Even as Elizabeth was grateful to hear that one of the non-military personnel supported her decision- he was probably the closest thing to a neutral opinion she'd receive in a situation like this-, she still couldn't help but wonder if there wasn't something she could have done differently.

"Well…" McKay said after a moment's awkward silence, "I'll just… get back to work, shall I?"

"Yes… of course," Elizabeth replied, briefly, nodding briefly at McKay as she continued to stare anxiously at the Stargate, a part of her wishing that it would start dialling even as the rest of her wished that it wouldn't; at least at the moment, she could _hope _that everything had worked out well with the mission.

Shaking her head in frustration, she turned around and began to walk back towards her office- she wasn't doing anybody any good right now- only to accidentally run into the young boy in the silver mask that she'd seen running around earlier.

"Oh- sorry, Doctor Weir!" the young boy said, looking apologetically up at her behind the mask. "Wex and I were playing, and we lost track of each other; I was just trying to find him-"

"That's all right… Jinto, wasn't it?" Elizabeth asked, smiling slightly at the young boy before her as she helped him to his feet. "No harm was done, and it's an easy mistake to make."

With the initial apology out of the way, she turned her attention to look curiously at the silver mask he was wearing. "If you don't mind my asking, what kind of mask is that?"

"It's the Phantom," Jinto said by way of explanation, removing it from his face and looking at her in surprise. "You mean you don't know him?"

"Should I have?" Elizabeth replied, smiling slightly at the young boy as she looked at him in a quizzical manner, only for the smile to fade at the genuine confusion on the young boy's face.

"The Phantom has defended this galaxy from the Wraith for the last few years, and he is said to do so from the city of the Ancestors using their power; how can you _not _know about him?" Jinto asked, his expression reminding Elizabeth of a child's face the first time a parent suggested that Santa Claus wouldn't be real. "He has been here for years; he would not leave the city, and he cannot _die _so suddenly…"

Deciding to remain diplomatic about the situation- given now little she knew about Athosian culture, she didn't want to risk causing problems by hurting a child's feelings, not that she'd do that deliberately in the first place-, Elizabeth simply shrugged and smiled slightly at him, privately noting his words about the Phantom and resolving to ask one of the adult Athosians about the individual in question as soon as she had the opportunity to do so.

"He's… he's here somewhere, I'm sure, Jinto; he… probably just doesn't want to reveal himself to us," she said, looking reassuringly down at the young Athosian. "We have stories of a lot of people like the Phantom back where we come from, and they all prefer to keep themselves secret from everyone else unless they have to tell them who they are, so that they can protect their families."

"Protect their families?" Jinto repeated, looking in confusion up at Weir. "But the Phantom has helped to protect so many people from the Wraith; why would he worry about his family?"

"Well… if everyone in the Pegasus Galaxy knew who the Phantom was, the Wraith would know where to find him and who to go after to hurt him while he was busy somewhere else," Elizabeth explained, silently thanking her brother for having a comics fan for a child; his ever-constant enthusiasm about every kind of superhero under the sun had provided her with a fairly thorough amount of background information regarding the motivations of some of the more prominent comic book heroes of the present. "He's probably here somewhere, but he doesn't want to let us know he's here until he's sure that we won't tell anybody else who he is; he's done this for so long that it's… probably hard for him to be sure of other people if he doesn't know them well."

"Oh," Jinto said, nodding in understanding before he smiled and placed the mask back on his face, clearly reassured regarding the Phantom's existence. "I _am_ sorry I ran into you before, Doctor Weir."

"Don't worry about it, Jinto; that's quite all right," Elizabeth said, smiling slightly at the young boy as he ran off once again, the mask on his face once more, only for the smile to fade as she reflected on the implications of what she'd just been told.

She had to admit, the idea of this 'Phantom' that Jinto had told her about did have a certain… well, 'appeal' was the only word she could find that seemed appropriate; it certainly went a long way towards providing her with answers.

After all, a figure in a mask who travelled around the Pegasus Galaxy doing what he could to protect people from the Wraith? While it might sound a bit like something from a comic book back on Earth, the fact that the man in question was rumoured to not only have access to Ancient technology, but, if Jinto had remembered the legend correctly, he was meant to do so from Atlantis itself?

If nothing else, it _would _go a long way towards providing her with answers regarding who had been using the DHD before their arrival, to say nothing of who had provided the fourth ZPM for the city and inserted that 'quirk' in the system to prevent them from even being able to send a message back to Earth to ask for assistance.

When she thought about it, it even accounted for…

Elizabeth's thoughts trailed off as she realised what had just occurred to her; the obvious implications had escaped her at first.

Could it be that the _Phantom _had been the one to program Atlantis to rise to the surface _before_ the power level in the ZPM had been depleted to dangerous levels?

In other words, was he _really _still inside the city somewhere, as she'd just told Jinto?

It would certainly explain what they'd discovered, but Elizabeth wasn't sure if she could even believe it. After all, the 'story' that Jinto had told her about the Phantom may sound real, but she had no real way of knowing if her earlier Santa Claus analogy was more accurate than even she had suspected. For all that she knew, the Phantom could just be an encouraging story that parents told their children to make them less afraid of growing up in a world where these 'Wraith' could attack them at any moment, and in reality any occasions where he'd supposedly saved the day were nothing more than lucky breaks or something like that.

Until she'd found an Athosian adult she felt comfortable asking about the story she'd just heard, she should consider that she had learned nothing new and move on.

Trying to force any further thoughts of the Phantom out of her head- until she knew something more detailed about that whole situation, she really had nothing that she could use to try and figure out what was going on here beyond speculations and what was essentially a child's story-, Elizabeth turned away from the Stargate and walked back to her office; after what she'd discovered, she definitely needed some time to think by herself.

She had only just reached the control room, however, when the Stargate suddenly began to activate, the blue chevrons illuminating around the large circle even as she changed her focus to getting to the control room as swiftly as possible.

Thoughts on the possible identity of the city's presumed recent inhabitant could wait; she had a situation to deal with at the moment.

"Offworld activation," Grodin said unnecessarily, glancing over at Elizabeth as she entered the room; presumably he simply wanted to confirm that none of them had done anything to trigger the current dialling sequence.

"Raise the shield," she said promptly, putting aside all thoughts of the Phantom and his possible purpose in Atlantis to one side for the moment; even if the theory was accurate, she had more immediate concerns to deal with right now.

As soon as the shield over the Stargate was activated, Elizabeth turn to look at McKay as he stood by

"Do we have an identification code?" she asked, hoping that he'd respond with 'Yes' and let her know straight away whether or not she'd sacrificed more good people in a failed rescue attempt.

Glancing at a nearby laptop, the scientist shook his head.

"Nothing yet," he said apologetically, leaving Elizabeth to stare anxiously at the Stargate before her, her fears about the team once again hitting her practically full-force.

Right now, all she could do was keep her fingers crossed and hope that she wasn't about to witness proof that the rescue attempt had failed and their enemies now had the 'gate address to Atlantis (The shield would protect them from an attack in that direction, of course, but keeping it on all the time would be a _definite _drain on power).

After a few anxious, nerve-racking moments, McKay finally spoke once again, turning around to look at her with an expression that almost looked like a grin.

"I'm reading Lieutenant Ford's IDC," he said, prompting a relieved sigh from Elizabeth as she glanced over at Grodin; at least that was _some _encouraging news.

"Let them in," she said, nodding at the technician, shifting her gaze back to the Stargate just as the shield over it was lowered. For a moment, nothing happened- not that Elizabeth was too worried about a few seconds' delay; given that the gateships were still new to them it was only natural that they'd take a while to properly manoeuvre them through the Stargate-, three bursts that looked like some kind of energy weapon came through the wormhole, striking the stairs and wall opposite and forcing some of the staff to dive for cover.

"Give them a few more seconds!" Elizabeth yelled as she saw Grodin reaching over to activate the shield; after waiting this long to find out if the mission had succeeded or failed, she wasn't about to close the shield on them until she knew either way.

A few seconds after she'd issued that order, the gateship came racing through the Stargate, only to immediately stop just yards into the Gateroom. Even without being a flyer herself, Elizabeth couldn't help but be impressed at the inertial dampeners the ship seemed to possess; it had halted at an extremely rapid speed, and yet, from what Elizabeth could see, nobody had so much as jolted in their seats inside the ship.

"_Reactivate the shield_!" she yelled over at Grodin almost as soon as she'd registered that the gateship had come to a stop, the shield automatically raising just in time for three loud thuds to take place.

Despite the simplicity of the sounds, Elizabeth couldn't restrain a slight wince as she saw the impacts through the shield; evidently, some of the 'Wraith' had attempted to follow the gateship back to Atlantis.

_Well_, Elizabeth mused to herself, as the gateship rose upwards towards the hanger, _if we weren't at war with the Wraith before, we certainly are now_.

She had to admit, her time in the Pegasus Galaxy was clearly _not _going to be what she'd expected.

* * *

A few hours later, the expedition members gathered together with the Athosians in an unofficially-declared 'getting to know you' party held in the main area of the city, Elizabeth stood at the balcony and looked out at the vast ocean before her, reflecting on the mission report she'd received from Colonel Sumner.

It hadn't gone well, to put it simply. The gateship had operated like a dream, allowing them to track the Wraith to a large ship on the planet's surface and providing them with what Lieutenant Ford had named a 'Life Signs Detector' that they were able to sue to track the captives once inside the ship. Having recovered the Athosians and some of the team from a cell inside the ship- planting C4 explosives at various points throughout the ship to better effect an escape in the process-, Sumner and Ford had gone to try and track down Captain Gemmel and an Athosian who had been taken from the cell earlier.

What they had discovered had not been a pretty sight; as far as Colonel Sumner could determine, these… _Wraith_… had the ability to literally drain the life-force from human beings and use it to sustain themselves. When they'd discovered the main chamber where Gemmel and the Athosian had been taken, the Athosian had been reduced to a withered husk that looked like a corpse that had been dead for some time, and Gemmel, according to Sumner's description, looked like he was a half-starved man in his late eighties.

Sumner didn't feel like he'd had a choice; he knew that there was no way that Gemmel would want to live like that, and he could see no way of restoring him to what he had been. With no other way to help his second-in-command, Sumner had been forced to shoot him, Ford subsequently killing the Wraith who had fed on him with one of the Wraith weapons.

The results, as far as they could tell, hadn't been encouraging. According to Ford and Sumner, as the Wraith had died she had revealed that she was merely a 'caretaker' for a large number of dormant Wraith in the ship, with multiple other ships like hers spread out throughout the galaxy… and, with her demise, the other ships in the galaxy had been activated, along with all the Wraith on board them. Sumner, Ford and the remaining former prisoners had barely managed to make it back to the gateship before the entire sky was filled with the dart-like form of the Wraith ships, and even then it had been touch-and-go in the resulting space battle for a moment before they had managed to get through the Stargate.

To say that Elizabeth was happy with how things had turned out would be inaccurate; they had not only triggered _another _war with a powerful alien race, but they had apparently significantly affected the status quo that existed in this galaxy by prompting the race in question to 'wake up' possibly centuries before it was meant to do so.

On the other hand…

Elizabeth could hardly blame Ford for doing what he'd done; at the time, the female Wraith had seemed to be the more immediate threat, and there'd been no way of knowing the consequences of their actions. He'd made a decision based on the heat of the moment, using the facts he had available to him, and it hadn't worked out; it was tragic, but it wasn't like there was anything they could do about it now. All she could do was make sure that Sumner selected a well-balanced team for his own trips through the Stargate- if they were going to fight against the Wraith, they were going to do it properly-, that the rest of the military teams that were selected had a decent balance of scientists and military men, and they were essentially sorted.

"Doctor Weir?" a voice said from behind her.

Glancing back, Elizabeth smiled slightly at Teyla, the woman who Ford had introduced to her as the leader of the Athosians; she hadn't had much of a chance to talk to the woman yet, but what she'd seen had given her the impression of someone she would find it easy to get along with.

"Hello, Teyla," Elizabeth said, smiling slightly back at the woman as she moved along on the balcony to give the Athosian woman something to lean on. "How are your people doing?"

"They are… as well as could be expected," Teyla replied after a moment's pause to process what Elizabeth had said; the Athosians were easily picking up some of the more common details of their new allies' language, but Elizabeth supposed that it was hardly unexpected that some details would take a while to become second nature to them. "Many of them are anxious about being within this city; some feel that the ghosts of the ancestors still remain…"

For a moment, Elizabeth contemplated leaving the opening that last comment gave her for a more convenient moment, but decided against it. After all, she had come this far;

"Would these ghosts include… the Phantom?" she asked, looking curiously at Teyla as she spoke, the better to judge her reaction to the comment.

Although a moment's silence followed that comment, Elizabeth was relieved to note that Teyla didn't look at her like a grown woman talking about the Easter Bunny while looking totally serious.

On the contrary, if anything, Teyla looked almost… startled?

"How… how do you know of the Phantom?" she asked, looking at Elizabeth in confusion. "I thought that your people were new to this galaxy; you had not even heard of the Wraith before coming here…"

"Let's just say I saw a strange mask on a child and wondered what inspired it," Elizabeth replied, smiling slightly as she glanced back at where Jinto was currently standing beside his father before turning back to look at Teyla. "What I want to know is… is there any truth behind the story?"

After a moment of silent contemplation, Teyla nodded slightly to herself and turned back to look at Elizabeth.

"There is a significant amount of information available about the Phantom, Doctor Weir; where would you prefer to start?" the Athosian leader asked.

Even amid the other issues surrounding her, Elizabeth smiled at the thought of getting at least some answers regarding this private mystery of hers.

Maybe, once she knew more about the Phantom, she'd have a better idea of how to deal with the possibility that he might be somewhere in the city…


	5. Mystery After Gala Night

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Bonus points to anyone who notices what's different about Elizabeth's conversation with Doctor Grodin in this chapter _before_ they encounter McKay and Ford

The Phantom of Atlantis

A couple of days after the Athosians' arrival in Atlantis, as Doctor Elizabeth Weir sat in her office, Colonel Sumner and Lieutenant Ford practiced on the shooting range, Teyla Emmagan helped her people adjust to their new home, and Doctors Rodney McKay and Carson Beckett attempted to perfect a process to give non-ATA-gene positive expedition members the ability to control Ancient technology, a figure clad in a black cloak and a silver mask crouched in his old observation hole in the tower and watched Elizabeth as she sat in her office.

He had to admit, it was good to see that he hadn't misjudged her at the beginning; she may not have been a military woman by nature, but she was nevertheless viewing her current situation from a military standpoint that he could easily approve of, even if he felt her unease about the Athosians was unwarranted.

He'd visited the planet once or twice (Using a cloaked puddle jumper, naturally), and he knew for a fact that none of them were Wraith worshippers; indeed, none of them would so much as even _think _of doing such a thing. Unlike some of the cultures he'd encountered in his time here- the Wraith worshippers aside, the Olesians, who just sat back and let the Wraith have anybody who stepped outside the rules of the little verging-on-Big-Brother-style regime they'd set up there, would always get on his nerves- the Athosians were genuinely good people, and he would always remain grateful that they, rather than anyone else, were the first civilisation that the expedition had made contact with.

In many ways, the two were exactly what the other needed; the Athosians provided the expedition members with local knowledge of both the civilisations and the food to be found in this galaxy, and the expedition provided the Athosians with a more secure location than the original Athos. He'd seen them settle in to work with each other so far, and they had done well; he had a strong feeling that things were going to work out well for the expedition as they began to settle in to their new home.

Now…

Taking a slight breath to prepare himself for his next move- what he was about to do would officially end any possibility he had of keeping his existence a total secret, after all-, he turned around and returned to the service tunnels that he'd used to access the area in the first place.

It was time to give Elizabeth his little discovery; if nothing else, it would make _him _feel better to know that she had it on her from this point onwards.

He just hoped he'd judged what her reaction to it would be correctly; if he was wrong, than his time in Atlantis was going to become _far _more complicated than he was prepared to deal with at the present moment…

* * *

Unaware of her silent observer as she sat in her office, Elizabeth's attention was current focused on the recent discoveries of their MALP excursions to date while trying to determine where would be the most appropriate location to send one of their teams to, to say nothing of considering the structure of the teams in question to see if there were any changes that she could suggest should be made to them.

She had to admit that, if nothing else, Colonel Sumner had put together a fairly effective collection of men and women when selecting his teams for offworld travel, particularly when selecting his own. Despite the lieutenant's own doubts about himself after killing the Wraith hive-keeper, Sumner had decided to keep Lieutenant Ford on the team to provide him with another military man to balance out the other two members; the lieutenant had, after all, displayed great presence of mind in coming up with a means of killing the Wraith when under pressure and conventional measures had failed, even if it had turned out to be a bad decision. Acknowledging the benefits of local knowledge of the Pegasus Galaxy and the need for a science expert in the event of them discovering any Ancient technology during their travels, Sumner had also selected Doctor McKay to serve as the team's scientist and Teyla Emmagan as a guide and unofficial diplomat.

All in all, Elizabeth had to admit that he'd chosen well; Teyla still needed some lessons in understanding Earth military weapons and tactics to ensure that she didn't unintentionally jeopardise one of Sumner's plans due to her not knowing what he was attempting to do, and McKay still needed to learn to pull his weight more in their shooting and hand-to-hand training sessions, but that aside the group was generally settling in with each other fairly well.

Now all Elizabeth needed to do was work out how to deal with the fact that she potentially had the Pegasus Galaxy's resident superhero hiding out in her city without anyone knowing about it.

'Superhero'…

On the surface of it, it was such a childish term- mention it anywhere back on Earth and people automatically thought of men and women in spandex costumes beating up criminals and saving people's lives from impossible situations-, but Elizabeth could think of no other term to describe the Phantom after what Teyla had told her about him.

Having appeared seemingly out of nowhere over a decade prior to the arrival of the Atlantis expedition, stories of the Phantom seemed to have spread throughout the Pegasus Galaxy ever since. Nobody was ever entirely sure how he did it, but it seemed that, ever since his first appearance, whenever the Wraith were known to be attacking a village that had little to no chance of effectively fighting back, glowing golden lights were always launched at their ships from nowhere, eliminating the ships and ending the Wraith's attack in a matter of moments. Sometimes, if some damage had been done to the location where the attacks had taken place, a figure clad in black clothes with a silver mask covering most of his face would appear on the ground to aid in the recovery of anybody who might have been trapped or injured in the attack, but with the last of the injured recovered he vanished without even waiting to be thanked. Nobody had ever been able to determine why the Phantom wore the mask that had become his most defining characteristic, and Teyla had no theories to offer Elizabeth either. Whether it was a simple disguise or served some other purpose, nobody could say; even exact descriptions of the mask seemed to vary, as nobody had ever managed to come close enough to see what it looked like beyond the facts that it was silver and seemed to cover most of his face.

On a more positive note, however, the more Elizabeth turned over the facts that she'd gathered about the Phantom in her mind, the more sense it seemed to make, particularly when she considered some of the Ancient technology they had discovered so far. Discovering trapped victims of a Wraith attack would practically be child's play with the use of a 'Life Signs Detector', and according to Sumner and Ford's reports of the recent rescue, the gateships used drone weapons much like had been deployed against Anubis's ship from the Antarctic base back on Earth, which would certainly account for the 'golden lights' that the Phantom was meant to use against the Wraith.

Admittedly, they had yet to discover anything that might give the Phantom the ability to know when the Wraith were mounting an attack, but Elizabeth was fairly certain that this last fact didn't mean anything; she was fairly sure it was little more than a coincidence. After all, it wasn't outside the realm of possibility that the occasions where the Phantom provided aid against the Wraith occurred simply because he visited those planets at approximately the same time as the Wraith ships arrived, and people simply never heard about the attacks where he wasn't involved because…

Elizabeth halted that line of thought instantly, not liking where it was going in the least; the thought of innocent people dying in the manner that had been described to her by Sumner and Ford wasn't something she felt like contemplating right now.

Sighing, she leant back in her chair for a moment, only to change her mind and leave her office; maybe a walk would help her think on what she'd learnt about the city's possible 'owner' better than simply sitting around.

* * *

As she walked through the corridors of what she was already beginning to think of as 'her' city- even as a part of her tried to remain cautious in case the 'Phantom' was real and expressed a desire for them to depart-, Elizabeth allowed herself some slight satisfaction as she took in her staff's continued efforts to sort out the equipment they'd brought along from Earth and work out how to incorporate it into the city's systems, or at least where to place it now that they'd had more opportunity to explore the city. To date, Elizabeth and Sumner had decided to confine the expedition to the area immediately around the control tower in order to limit any risks of leaving people behind in case they needed to evacuate Atlantis on short notice for some reason (Exactly where they'd go instead had yet to be determined; finding an appropriate planet to set up an Alpha Site would have to be one of their first priorities once they were settled in), but with the Athosians to take into account, they'd need to step up their exploration schedule as soon as possible to try and find enough rooms for everybody to be comfortable in.

"Doctor Weir!" a voice said from off to one side as Elizabeth walked down one of the corridors. Glancing back in the direction of the voice, Elizabeth smiled slightly as she saw Doctor Grodin walking towards her. The young man's honest enthusiasm about their discoveries in the city was something that Elizabeth was always grateful to hear; McKay may have been just as enthusiastic on being in Atlantis, but his habit of trying to take exclusive credit for the discoveries they'd made somewhat negated the pleasure she felt at seeing an inquiring mind find the answers to various questions.

"At ease, Doctor," she said, silently wondering even as she spoke when she'd begun to so easily slip into military vocabulary; even after so short a time in the Pegasus Galaxy, a part of her was already waiting for the other shoe to drop and the Wraith to find them. "Have any of the teams discovered something since we last spoke?"

"Well," Grodin said, as he turned around and began to walk back towards the control room, prompting Elizabeth to follow him, "some of the other scientists and myself have discovered what seems to be the Ancients' water treatment plant; as far as we can determine, it works by desalinizing the sea water and storing them into tanks big enough to supply the whole city.

"Good," Elizabeth said, nodding briefly in approval at him. "So fresh water won't be a problem."

So long as she avoided thinking about the fact that food was still going to be an issue until they were able to stop the shield activating whenever they dialled Earth, she could at least rest easy on that particular score.

"It seems that some Ancient technology requires the use of the active gene," Grodin continued as he walked. "Other things merely require initialisation; once activated, like the control room, anyone can push the buttons to make it work-"

Further conversation was temporarily interrupted as three Athosian children hurried past them, one of them- Jinto, Elizabeth noted with a slight smile- wearing the silver mask of the Phantom as he led the others.

"Good morning, Doctor Weir," Jinto said briefly as he and his friends hurried between her and Grodin.

"Good morning," she called after him, "and careful!"

As soon as the children had vanished around another corner, Elizabeth assumed a more professional expression and glanced back at Grodin. "I think we need to dedicate some recreational areas."

"Agreed," Grodin confirmed, nodding in agreement at her as they continued to walk up the stairs.

"And," Elizabeth added, indicating a box of equipment slightly further along the corridor they had just come along, "we certainly need to clear the hallway and get everything put away as soon as possible."

"Of course," Grodin confirmed, as they continued up the stairs. "We're still in the process of making sure that everyone's been assigned living quarters; Colonel Sumner seems to be taking his time OK-ing enough space."

"Well," Elizabeth continued as they finally entered the control room and she began to walk back towards her office, "the safety and security of this expedition are his-"

"OK, I'm ready!" McKay's voice suddenly said from off to the side. Glancing in the direction of the voice, Elizabeth just had enough time to see Doctor McKay and Lieutenant Ford standing on the balcony outside the Atlantis conference room before Ford literally shoved McKay over the balcony, sending him hurtling towards the floor of the gateroom to hit it with a powerful thud.

"Woah!" Ford said, grinning slightly as he glanced over at where Elizabeth and Grodin were now standing at the balcony outside the control room. "Did you _see_ that?"

"Yes…" Elizabeth said, looking at Ford and wondering if he'd had some kind of pre-existing mental imbalance that the SGC psychiatric evaluations hadn't picked up on beforehand. "What the-?"

"I'm fine," McKay suddenly said, picking himself up from the floor as though nothing had happened, raising his hands reassuringly as he looked up at them, revealing some kind of glowing green… Elizabeth could only think of it as a gem, even as she knew that it was clearly more than just a jewel McKay had found somewhere… on his chest.

Her curiosity roused, she turned around and headed for the stairs leading down towards the floor of the gateroom, Grodin close behind her as Ford hurried over to join them.

"Look!" McKay said, grinning broadly as he indicated the device on his chest. "Beckett's gene therapy worked; I was able to activate this! It's a, uh, personal shield; acts like a protective skin, and it must have inertial dampening features too, because-" he indicated the area where he'd just landed with one hand, "-I didn't feel a thing. Watch this."

Before Elizabeth could ask him to elaborate further, McKay had turned to look at Peter, a clearly eager expression on his face. "Hit me."

Elizabeth wasn't sure what startled her more; the fact that McKay had just asked someone to punch, the fact that Grodin didn't seem to hesitate before doing so, or the fact that, the second his fist made contact with McKay's face, a greenish energy shield appeared around McKay- accompanied by a faint sound that reminded her of the traditional noise made when Ancient technology activated.

"AHHowww… GOD!" Grodin yelled, clutching his hand as some of the Athosian children behind him laughed at the sight (Elizabeth had to admit, there was a part of her that found it hard to restrain a slight smile herself).

"You didn't have to swing so hard," McKay said nonchalantly before he glanced over in her direction. "And notice he didn't even hesitate."

"I'm still trying to understand how you thought it was a good idea to test this device by having someone throw you off a _balcony_," Elizabeth stated, trying to get the conversation

"Oh, believe me," McKay said, grinning slightly at her as he indicated the balcony once more, "that's not the first thing we tried."

"I shot him," Ford said, a broad grin on his face as he looked over at Elizabeth, the grin only fading slightly as she stared incredulously at him. "It was just in the _leg_."

As Elizabeth turned back to look critically at McKay, the scientist simply shrugged and grinned back at her.

"I'm invulnerable!" he said happily.

"Aren't you the one who's always sprouting off about how proper and careful scientific procedure must be adhered to?" Elizabeth asked.

"In-vul-ner-able," McKay replied in a sing-song voice, clearly unconcerned about his superior's evident unhappiness with his actions.

"Alright…" Elizabeth sighed, deciding to give the matter a rest until a better opportunity to discuss it came up, "take it off; let's go have this meeting."

"Just jealous…" McKay muttered as she began to walk up the stairs.

"Oh yes; _green _with envy," she said, turning back to look at him as she paused mid-way up the stairs. Just as she turned around, McKay was raising his hand to his chest…

Only to be unable to touch the shield in question as the force field prevented him from reaching it.

"Oh," he said, as he attempted to reach the device again, "this could be a problem…"

As the small group that had gathered around him earlier turned to look at the scientist, McKay once again attempted to reach the device, only for the shield to once again block his hand as he looked anxiously up at them. "I can't get at it."

Raising an eyebrow, Ford reached out in an attempt to grab the device himself, only for the same thing to happen; his hand could make contact with McKay, but it couldn't actually touch his skin.

"Just checking," the lieutenant said, raising his hands apologetically as McKay glared at him.

"All right…" Elizabeth sighed, quickly going over the possible ways to deal with this new problem. "Doctor Grodin, please accompany Doctor McKay to the medical wing; maybe Doctor Beckett can offer some suggestions about whether or not this is related to the gene therapy. Lieutenant Ford, you're with me; Colonel Sumner and Teyla are waiting for us in the briefing room."

* * *

An hour later, the meeting with Sumner on base security over and the self-destruct codes should the base ever be penetrated assigned to their respective owners (McKay stating that they not bother offering him one due to his current predicament; Elizabeth strongly wished he wouldn't go on about that as much as he did), she was once again heading for her office, her mind going over everything that had been discussed in the recent meetings in case she'd missed something important at the time.

In general, she felt that the situation was going well. Admittedly, she was still uncertain about trusting Teyla until the issue of whether or not one of the Athosians had tipped the Wraith off to their arrival in the first place had been satisfied one way or the other, and they were still no further along in determining the password that would allow them to shut down the shield whenever they tried to dial an address outside of this galaxy, but those questions aside the expedition were settling in fairly comfortably. The naquadah generators that they had brought with them from Stargate Command were helping to limit the amount of power being used by the ZPM, the search for living quarters was coming along well, and they'd already managed to track down rooms that could serve as a medical wing, an armoury, a mess hall, and even food storage.

If it weren't for the issue of the head of the science division facing death by starvation due to his apparent inability to calm down enough to turn his personal shield off- and Elizabeth was _convinced _that it was McKay's subconscious fears keeping that thing on; she wasn't a medical doctor but she was confident that the Ancient gene therapy wouldn't just grant someone the ability to turn the technology on without being able to turn it off-, Elizabeth would even go so far as to say that they already had the city running perfectly.

As she reached her office and moved to sit down in her chair, thoughts of McKay's current predicament occupying her thoughts- was there anything that they could do to make Atlantis more comfortable in the short term that might ease McKay's subconscious fears about their current situation enough to allow his subconscious to turn the shield off?-, she saw something on the table, and her eyes widened.

It was another Ancient Shield Device…

With a _note _attached?

Raising a confused eyebrow, Elizabeth picked up the note and studied it, instantly discovering that it almost presented more questions than it answered. Not only was it written in English- which effectively ruled out anyone but the rest of the expedition as being the ones to write it in the first place- but it stated on it, in clear, albeit sketchy letters, as though the person who'd wrote it hadn't done anything like this for a while,

"_This one works for you_.  
_Keep it secret, and be safe…  
__for me_."

_What_? Elizabeth thought to herself, looking in confusion at the Ancient shield she now held in her hand.

What could the writer have meant when he said that it would 'work for her'? She didn't even have the Ancient gene and had yet to authorise full distribution of the gene therapy; how could _she _be expected to operate this thing?

Still…

Maybe it was just the tales she'd heard of the Phantom since she came here- the idea of one man managing to make that kind of impact on an entire galaxy, even if not _every _tale she'd heard about him could be true, was somewhat inspiring in its own way-, but there was a part of that was beginning to feel that, when it came to Atlantis, it was possible that _nothing _was impossible.

Despite everything she knew about Ancient technology telling her that this wasn't going to work, Elizabeth picked up the shield device and, after a moment's thought, placed it on her chest, the shield turning bright green as soon as it came in contact with her jacket.

Blinking in shock as she stared at the device, Elizabeth quickly reached up to remove it, grateful when it simply shut down and came away in her hand rather than preventing her from taking it off as its counterpart had for McKay. Whether this device was simply easier to turn off than McKay's was, or she simply had a greater degree of control over her subconscious mind than McKay did, Elizabeth wasn't sure and didn't feel like questioning in any great detail.

All that _did _matter was that somebody had given her an Ancient shield device that she could somehow control despite her lack of an Ancient gene, they wanted her to keep its existence a secret, and they wanted her to stay safe… for _them_?

Elizabeth was rapidly beginning to feel like she'd ended up in the middle of a bizarre mystery novel; every discovery that she made only left her with even more questions to be answered about the city and its near-mythical 'guardian'.

Who could have left this shield for her?

How was she able to control something that, according to McKay and Grodin, required the Ancient gene in order to work at all?

And more importantly… why would whoever have left the shield here for her in the first place be particularly concerned about _her_ safety over everyone else they might have given the shield to?

* * *

AN 2: If anyone's wondering about how Elizabeth can work the shield device despite not having the Ancient gene, I took my inspiration from 'Irresponsible', when Lucius Lavin mentioned that he managed to get his one working by tracking down someone with the Ancient gene and getting them to activate it for him, subsequently using it for himself. Since Lucius was able to turn it on and off- as well as permit John to use it when he faced off against Koyla and his men - without having the Ancient gene himself, I'm assuming that, like most Ancient technology, the gene is simply required to turn the shied on in the first place and isn't required in the long term. I'm also assuming that McKay's belief in 'Hide and Seek' that the shield imprints on the wearer is, like turning the thing on or off, mainly controlled by the user's will rather than being a fixed fact of the shield's design; if the wearer _wants _someone else to be able to use the shield, the shield will automatically program itself to respond to that other person


	6. The Curtain Falls

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

As he slipped the silver Phantom-mask over his face- the lack of any trees or similar things that could provide him with makeshift weapons was something about the city that Jinto found disappointing, but it was a minor thing in exchange for safety from the Wraith-, Jinto smiled slightly as he hurried along the corridors of the city of the Ancestors, his eyes constantly on the alert for any sign of Wex.

The city of the Ancestors may be a confusing place to understand, but the amount of good hiding places within it- to say nothing of the Wraiths' current lack of knowledge of its existence- more than made up for that, as far as Jinto was concerned. All the numerous corridors and rooms… all the incredible machines and sights that could be seen… the amusing tales that Lieutenant Ford and some of the younger civilian scientists had to tell…

As far as Jinto was concerned- and, from what he could see, even the people of Earth felt at least some degree of that same awe he felt-, it was the most incredible thing he'd ever seen.

As he continued to hurry through the corridor, his eyes constantly on the alert for Wex in the Wraith-mask, he noticed a large sealed door in front of him that struck him as a likely hiding-place that Wex might have used. Walking over to the door, he touched the blue-and-grey rectangular shape on the left that opened the doors, but the other side of the door was revealed to be nothing more than a small room containing boxes from Earth…

Jinto froze.

He had heard something…

It sounded somewhat like the wind, but closer and stronger than any wind he had experienced back on Athos.

For a moment, Jinto felt a shiver of unease down his back.

Could it be that the Phantom _was _here…?

After another such sound occurred, Jinto didn't hesitate; he turned around and entered the room before him, the door swiftly closing behind him as he tried to remain silent in order to avoid attracting the attention of whatever was out there, before his eyes registered a faint glow behind him.

Turning to look in the direction of the glow, Jinto was surprised to see what looked like a map of the city of the Ancestors- based on the images he had seen on the walls of the main control room- on the wall behind him. Curious at its appearance, he reached up to touch it, and suddenly the door opened to reveal a totally different scene in front of him compared to the one that had been outside the door when he had entered this room mere seconds ago.

Confused but nevertheless eager to find out what had just taken place, Jinto cautiously stepped out of the small room to study his new location. It was a decent-sized room, about as large as the main hut in the village back on Athos, with two of the large rectangular things that Doctor Weir had called 'control consoles' immediately opposite the door he had just entered by. Apart from the consoles, the only other thing inside the room was a table off to the right of the door he had entered by, upon which stood a large, dark brown cylindrical device with glowing yellow lights around the middle and what looked like two stones on top of it, the lights glowing slightly even as Jinto stared at them.

Almost without knowing what he was doing, Jinto found himself walking slowly towards the device in question, one hand slowly reaching out to touch it as he drew closer to it. His hand was drawing closer… it had touched one of the stones…

No sooner had Jinto made contact than a thin black burst of what looked like smoke emerged from the device, swiftly spreading out until it went from being barely as thick as Jinto's arm to spreading out around the device he had just touched. Briefly the young Athosian attempted to touch it once again, but the second his arm made contact he was left with a sudden chill, causing him to yank his hand back as he stared in confusion and horror at the sight of the dark cloud before him, growing and spreading out of the machine before him, reminding him of the illusions generated by the Wraith if the Wraith were able to affect more senses than simply your eyes and ears…

Then, mere moments before the creature made contact with him once again, a hand reached out and grabbed his wrist, hauling him away from the creature before him before shoving him into a corner of the room.

The initial fear at what had just taken place wearing off, Jinto slowly turned his head slightly to see who had discovered him, only for his eyes to widen as he took in the sight of the figure standing before him, one hand holding his shoulder while the other hand was raised to his lips in a silencing gesture.

If he hadn't seen the man before him with his own eyes, Jinto would never have believed what was happening to him at that moment.

_It was _him…

* * *

Hearing the sound of hurried footsteps outside her office, Elizabeth quickly slipped the shield device into her pocket as she stood up; until she had more to go on than suspicions and half-certainties, or until she discovered anything that at least had the potential to be dangerous to the expedition if left unrevealed, she wasn't going to report anything Phantom-related to Colonel Sumner or his team.

For a moment, as Ford hurried into her office, Elizabeth allowed herself a moment of relief- Ford, at least, was less likely to be automatically suspicious of her moving something around on her desk- before she noticed his anxious expression.

"Lieutenant?" she asked, looking anxiously at him as she stood up behind her desk. "What's wrong?"

"It's Jinto, ma'am," Ford replied. "He was just in this lab in an area we hadn't explored yet- from what we can gather he activated some kind of teleporter to get there-, and…"

For a moment, Ford was silent, as though uncertain how to say what he was about to say, before he finally seemed to come to a decision. "Well, he claims that someone he calls 'the Phantom' saved him from something that he was told is a kind of 'energy leech' that will drain our systems of power if we don't figure out a way to get rid of it."

Elizabeth had no idea what to react to first; the news that there might be some kind of creature active in the city, or the discovery that her earlier theory was right and that the Phantom actually _was_ still on Atlantis.

"The Phantom?" she asked at last, deciding that her best bet at the moment was to feign confusion about the existence of the city's possible inhabitant unless she, for some reason, had reason to reveal what she'd discovered about him already. "Who is that?"

"Some kind of major hero for the Pegasus Galaxy who's supposed to have lived here and been fighting against the Wraith for the last decade or so; Jinto wasn't able to give me anything more specific than that, and Colonel Sumner has decided to focus on the creature for the moment," Ford responded quickly (Elizabeth had to admire the diplomatic way the young lieutenant had phrased his response; letting her know that he disapproved of her focus on the Phantom as opposed to the creature in her response to his information without actually being offensive about it). "Colonel Sumner's expressed some doubt about the creature's existence, but he's got Doctor McKay checking the lab that Jinto transported himself to just in case there's something in the story."

"Where's Jinto now?" Elizabeth asked, as she arrived in the control room where Sumner, Grodin and McKay were already waiting, each of them looking in her direction as though awaiting their next order.

"With his father," Sumner said briefly, before he turned his attention over to McKay. "Doctor McKay, you said that you'd found something about that… creature Jinto mentioned?"

"Well, it might not really be _anything_," McKay said- Elizabeth was relieved to see him do something that wasn't related to his potentially imminent death- as he turned to indicate one of the monitor screens nearby him, "but I've been noting some strange energy readings in some parts of the city-"

Mid-sentence, the lights around them suddenly dimmed with a low hum before returning to their normal intensity, leaving Elizabeth glancing over at Rodney for an explanation; she was fairly certain Ancient technology wasn't meant to just 'cut out' like that.

"Uh… given what we learned from Jinto, those _seem _to be connected to the creature," McKay said by way of explanation, although his face clearly showed his scepticism of Jinto's story; whether it was because it came from a child or because he didn't like the concept of the Phantom Elizabeth wasn't sure. "If it's what this… Phantom… guy told Jinto it was," (His hesitancy at that point answered Elizabeth's earlier question; it was the Phantom part of the equation he had trouble dealing with more than anything else) "this thing should apparently be capable of absorbing energy from our active systems as a source of sustenance; it can probably also cause minor power fluctuations in its immediate vicinity, but our main problem is, as I said, its need to take energy from the city's power supply in order to sustain itself."

"It absorbs energy from our power supply?" Elizabeth repeated, looking anxiously at McKay as the implications of that statement sunk in.

If this creature made it to the Zero Point Module chamber… containing their only working ZPM and hence their only working means of defending themselves if they were discovered…

"Don't worry, it's already sorted; I had my staff disconnect the ZedPM as soon as Jinto had told us his story," McKay said, holding up a reassuring hand as he spoke. "Just because I didn't totally believe Jinto's story doesn't mean I was going to be stupid; if this thing managed to drain our ZPM, we'd be in _serious _trouble if the Wraith ever manage to get here, and if it wasn't…"

He shrugged casually. "Well, if it turned out to be nothing more than a false alarm, we're not really using it at the moment, and plugging it back in would be easy enough; better safe than sorry, after all."

"OK, so… based on what Jinto told us he learned from this 'Phantom', what do we _know _about this creature?" Elizabeth asked, turning to look at Sumner and McKay.

"Well…" Sumner said, clearly uncertain about relying on something that had been told to them by a boy from a source they knew nothing about- Elizabeth's knowledge of Sumner's character made it easy for her to determine that it was both of those factors rather than one over the other that was causing his problem with the situation at the moment-, but nevertheless lacking any other options at the present, "According to what Jinto learned from this 'Phantom', it was the result of an Ancient experiment while they were attempting to learn how to Ascend; we don't know anything more precise than that about its origins at the moment. When the Ancients realised what it was capable of, they trapped it until they could figure out something better to do with it. As Doctor McKay explained, it also appears to feed off energy sources, which would certainly account for the power fluctuations we've been experiencing; this creature's almost certainly going after our naquadah generators."

"Have we tried shutting the generators down?" Elizabeth asked McKay.

"I thought about it, but it wouldn't really work; you need to take into account that people give off energy too," McKay pointed out. "Granted, it's negligible compared to that of a naquadah generator, but… you take away this thing's only other source of food…"

Elizabeth could see his point; so long as this creature continued to focus on the generators, they might at least be able to work out a way of keeping it occupied without losing any of the expedition to it.

"OK, so we leave the power on," she said, nodding briefly at McKay before she turned back to Grodin. "Grodin, work on finding some way to track that creature and work out where it is; McKay, have you examined the lab where Jinto says he encountered the Ph- the creature?"

(Elizabeth could only hope that nobody had noticed her slip-up; the last thing she needed was for people to notice her ever-growing curiosity about the Phantom when Colonel Sumner's expression made it clear he disliked the concept of somebody operating in the city outside of his control.)

"I was just about to accompany Doctor McKay to the lab, actually," Sumner said, nodding briefly at Elizabeth before he glanced over at Grodin. "You heard the doctor; get to work."

"Yes, sir," Grodin said, unable to restrain a slightly sarcastic tone in his voice as he began to work (Not that Elizabeth could blame him for it; Sumner may be a good soldier, but his somewhat blunt manner towards the scientists and the Athosians took some while to get used to).

"Good," Sumner said in response, before he glanced over at Ford. "Lieutenant, get the men together in teams of two and begin a search of the city; if you discover the creature, report in but do not engage. Doctor McKay, let's go."

With that, Sumner turned and headed out of the control room, followed by McKay and Ford, the lieutenant swiftly heading towards the personnel quarters while Sumner and McKay headed in another direction that Elizabeth was fairly sure wouldn't lead them to where Jinto must have been playing; the Athosians' quarters were in another direction altogether.

"Is there any reason that Colonel Sumner is taking Doctor McKay in _that _direction?" she asked, glancing inquiringly over at Grodin; she didn't like feeling like she was being kept out of the loop when it came to matters in the city, even if Colonel Sumner was supposed to have final authority in the city when it came to military matters like their current situation.

"Oh, that leads to one of the teleporters that Jinto's discovered," Grodin replied, smiling slightly at her, only for the smile to fade as he took in the expression on Elizabeth's face. "He didn't mention them to you?"

"Well, Lieutenant Ford did mention something about teleporters, but at the time I was more focused on… other matters," Elizabeth admitted, already scolding herself for her inattentiveness; she'd been so focused on having the existence of the Phantom verified that she'd completely failed to pay attention to the less immediate matters than the existence of an energy-sucking creature in the city. "What do you know about them?"

"Well, based on what Jinto told us and the readings I was taking of the city at the time he accidentally released the creature, it would appear that there are multiple small teleportation 'booths'- for lack of a better term- located at various points around the city that allow the user to be instantaneously transported from one booth to the other when a location on a screen in the booth is activated," Grodin explained, an eager expression on his face at the implications of this discovery before another temporary dimming of the lights left him with a slightly more dejected expression on his face. "I'll just… get back to work now, shall I?"

"That would probably be for the best," Elizabeth admitted, nodding briefly at him before she turned back to her office. "Let me know if Colonel Sumner returns; I'll be in my office if I'm needed."

She may not have particularly liked the need to keep secrets- it was one reasons he'd left that message for Simon before she'd left for Atlantis; if she was going to go all the way to another galaxy she'd rather he didn't think she was just in Afghanistan or something like that-, but right now, with the Phantom's existence having been confirmed and Sumner's attitude towards that discovery making it clear that he disapproved of the idea, she didn't think it would be advisable to admit that she was returning to her office to pick up something that he'd apparently left for her.

It might not provide her with much protection, and she certainly wasn't going to use it just yet, but with an energy-draining creature at loose in the city, Elizabeth would definitely feel safer if she had that Ancient shield device on her…

* * *

A few minutes later, the device hidden away inside her inner jacket pocket, Elizabeth stood behind Grodin as he showed her an image of the city, blue dots with swirling outlines highlighting the naquadah generators as an indistinct pink shape drifted through the corridors.

"After I calibrated the city's internal sensors, pinpointing the creature was fairly easy," Grodin explained, smiling slightly as the creature advanced towards the nearest naquadah generator. "So far as I can tell, there's only one entity, making it relatively easy to keep track of. All I need to do is monitor its location and deactivate the generators whenever it comes too close to one, and we can keep it on the move while retaining our current power levels."

"Good," Elizabeth said, nodding in approval. "Keep at it until we come up with something more permanent."

She didn't voice her inner concern that they might be making the creature mad; with everything else she currently had to deal with, such as the growing likelihood that her own earlier interest in learning about the Phantom would come to Colonel Sumner's attention, the last thing she wanted was more problems to worry about…

"_Doctor Weir_," Colonel Sumner's voice said from over the radio, "_Doctor McKay and I have identified the entity's origins; could you join us_?"

"On my way," Elizabeth responded, nodding briefly over at a nearby marine before she departed; with this creature roaming the halls, regardless of how useless a P-90 might have been against it, she doubted Sumner would be happy if she started roaming the city without a bodyguard. Following the directions to the transporter that Grodin had provided her with earlier, she had soon used the device for the first time and was subsequently standing inside the lab that Jinto had been transported to earlier, Sumner standing behind McKay as the scientist tapped away at a laptop he'd brought down with him.

"Any luck?" she asked the scientist, noting the protective shield was still active; how much power could that thing hold?

"Well," McKay said, as he glanced up at her, "believe believe it or not. Jinto didn't touch anything of any consequence… other than that."

As he pointed at something behind her, he stood up and walked around towards what he had pointed at, leaving Elizabeth to turn and watch as the scientist walked up to a brown cylindrical device and pressed a switch that caused god lights to illuminate all over it.

"It has its own power source, like the Gateships," McKay explained, noting Elizabeth's slightly puzzled expression and apparently misinterpreting it.

"What is it?" she asked, looking critically at the man; the only reason she didn't criticise him for assuming she hadn't guessed about the power source was that she doubted he'd appreciate it given his current situation.

"Well," McKay replied, turning his attention back to the device, "from what I can tell, it served as some sort of containment vessel for the energy creature-"

"Until Jinto released it," Sumner commented.

"Well, it seems that way," McKay said, before he continued. "As I… well, as _Jinto_ told us, the entity's what's been causing most of our technical problems. It was captured by the Ancients while they were researching Ascension, suggesting that the process may not have been the purely spiritual matter we assumed it was based on Doctor Jackson's experiences; there may actually have been evolutionary intervention to get there."

"Their own form of gene therapy?" Elizabeth asked.

"Well, I haven't read all the notes," McKay said dismissively before he continued, "but what I do know is that the entity is energy; it feeds on energy forces. Quite frankly, we need to take this thing out soon; the more it feeds the bigger it gets, and the bigger it gets and the more deadly it will be."

Elizabeth definitely didn't like the sound of that; this creature was proving difficult enough to handle at the moment. If it got too large, it could theoretically engulf buildings; they had to contain it now while it was still of a manageable size.

"Is it intelligent?" she asked, hoping a diplomatic solution might present itself.

"Well, according to the research it _is_ sentient…" McKay admitted, before shaking his head resolutely. "However, I wouldn't recommend trying to talk to it; you'd have more luck with a great white shark. This thing is going to suck the power out of our generators- maybe even the ZPM if things get bad enough- and then it will kill us all."

Sighing slightly, Elizabeth shook off her dejection and turned her attention back to the matter at hand.

"All right," she asked, turning back to look at McKay, "what do we do about it?"

"Well, the energy's been trapped in here since before the ancients abandoned the city; it seems like that it's pretty mad," McKay explained, as he looked intently at the machine. "On a more encouraging note, it's also going to be hungry, which means that it might not be thinking _that _clearly about everything. Given that this device was designed to attract it, capture it and hold it for observation, there's still a chance we may be able to get it back inside; I'm just going to need a little more time to figure out how."

"'A little more time'?" Sumner repeated, looking intently at McKay. "You told me you had it already."

"Doctor?" Elizabeth stated, her tone making it clear that, if what Sumner had just said was indeed the case, McKay had better explain himself as soon as possible.

"Look, I just need to make sure that everything works the way I think it'll work; I've pretty much confirmed _what _it is already," McKay replied. "Essentially, it's a mouse trap; if I've understood the instructions, this button here causes the device to emit an energy signature that attracts the creature, while this one shuts it in."

With that said, McKay turned to look at the two of them, a slightly uncomfortable expression on his face. "The only downside is… someone's actually gonna have to be here to press the buttons."

Before Sumner could say anything to that, Elizabeth smiled slightly as an idea occurred to her that might solve at least one problem.

"Well, Rodney," she said, as she turned to face him directly, "you're still wearing the shield. Is there a chance that, if something went wrong, that would protect you?"

No sooner had the words left her mouth, the shield device on McKay's chest dimmed and fell off his chest, McKay instinctively catching it in his hand. For a moment he simply stared at it for a few seconds, but then, as though remembering what he'd been complaining about earlier, he pulled a protein bar he'd picked up earlier out of his pocket and began to chew on it with a look of supreme satisfaction on his face.

"I had a feeling," Elizabeth said, half to herself and half to Sumner, as she began to turn back to look at the device.

"What do you mean?" McKay's voice suddenly said indignantly from behind her. "Had a feeling about what? You think I _wanted_ it to come off just now?"

As McKay walked over to stand in front of her, Elizabeth was only just able to stop herself from smiling at his outraged expression, even as the effect was slightly ruined by the mouthful of protein bar. "You think I'm scared? I'm not scared! I'll stay; I'll do this!"

"No need, Doctor; I'll handle this," Sumner said, a faint smile on his face (Much to Elizabeth's surprise; she wouldn't have expected Sumner to be the type to ever smile).

"Well, it-it's just not working any more!" Rodney yelled, placing the shield device on Sumner's chest for a few seconds before pulling it back, still deactivated. "See; it doesn't work on you either!"

"I just _meant_ that it wasn't going to let you die," Elizabeth interjected, once again only just managing to stop herself from smiling; there was something rather amusing about seeing a scientist of McKay's alleged intelligence acting like a child.

"Well, it is _just_ a _coincidence_ that it happened to stop working now!" McKay continued, before he sighed in frustration. "_God_, I need a drink…"

"Go," Sumner said briefly, indicating the door beyond McKay. The scientist needed no further encouragement; he swiftly turned around and headed out of the room, leaving Elizabeth and Sumner to look briefly at each other before Elizabeth sighed and nodded.

"Well, Colonel, it looks like it's up to you," she said. "I'll get back to the control room and order the rest of the city to be powered down while you activate this machine; once the creature gets in close enough, it sounds like all you need to do is activate the machine and you're sorted."

"Affirmative, ma'am," Sumner said, nodding briefly at Elizabeth in response.

* * *

As he crouched in one of the many small passages that allowed him to travel through the city, he allowed himself a slight smile as he saw the Athosians lighting candles to keep the creature at bay; even as he doubted it would actually do anything to the thing, he could appreciate the need for some form of comfort, even if it didn't exist.

After all, wasn't that what he did every day? Maintain an illusion so he wouldn't have to face the reality of what he had become so many years ago…?

Shaking his head to force his attention back on track, he quickly went over everything he'd gathered about the current plan to eliminate that energy creature (He _knew _he should have dumped that thing when he had the chance, but it had just seemed too much effort to drag that thing all the way to the gateroom when all he had to do was not touch it to keep it from ever being a problem). In theory, the plan worked, but it failed to acknowledge one crucial detail; this energy creature was a non-corporeal Wraith, and he had never yet met a _single _Wraith, whether an individual or a group, that would fall for the same trick twice.

Hell, if the Wraith had been that stupid, he'd have taken out a _hell _of a lot more than just five hive-ships over the last fifteen years; as it was he kept on needing to change his attack strategies to accommodate whatever modifications they'd made to their hive-ships to protect the vulnerable areas he'd taken out the last time around.

No, this creature wasn't going to get stuck back in that old set-up again…

_Which means_, he reflected to himself, his fists clenched as he went over the only other alternative in his mind, _that I'm going to need to break the whole 'secrecy' thing I promised myself I'd create a bit sooner than I expected_.

He didn't like it, of course- he'd probably have the entire city virtually breathing down his neck trying to find him, unless he was very much mistaken in his assessment of Colonel Sumner's character-, but if it was a choice between being hunted and being driven out of the only home he'd had for the last couple of decades, he'd take being hunted; at least he knew the territory well enough to stay out of everybody's way in that scenario.

Glancing back at the control room to make sure Elizabeth was there- she was currently talking with that Doctor Grodin guy about something; she'd be safe enough there while he took care of things elsewhere-, he turned around and headed deeper into the tunnels, making for one of the nearest located naquadah generators.

He just hoped that he'd manage to time everything right; even if he had to confirm beyond all doubt that there was actually someone else apart from the expedition members inside the city, he _didn't _want to be captured just yet…

* * *

Even as she stood in the control room preparing to terminate the power throughout the city, Elizabeth couldn't help but wonder about what Grodin had just told her regarding the shield device (Why she was focusing on such a trivial detail, Elizabeth wasn't sure; maybe it was because she couldn't do anything else right now and so found it easier to focus on her own personal mystery).

If the shield devices 'imprinted' on the first person to activate them, how could she use that one that… someone (The Phantom?) had left in her office? Had McKay missed something in the files he'd discovered with the device, was something wrong with her device, or was there some other explanation she couldn't think of right now?

It may not have been an important question, but it was one that Elizabeth wished she knew the answer to…

"You ready?" McKay's voice said from behind her, his mouth once again apparently full as he sat down in a seat beside Grodin.

"You do realize that when we shut everything down, we're going to lose the sensors?" Grodin said, glancing up at Elizabeth as he spoke. "We're not going to be able to track it…"

"We have security personnel posted round the living quarters; at least we'll have some warning," Elizabeth replied, smiling slightly at Grodin before she leaned over to light a nearby candle. Noting McKay's quizzical expression, Elizabeth turned to look at him. "Teyla told the Athosian children that lighting a candle would help protect them."

"And you're doing it because…?" McKay asked, raising an eyebrow.

"It's going to get dark in here," Elizabeth replied simply.

McKay moved to turn on a flashlight that he'd acquired from somewhere, but Elizabeth shook her head. "Don't do that; the light may not generate much energy, but it would still be stronger than candles, and the last thing we want is to give this thing another target."

Sulking slightly, McKay simply placed the flashlight down on the floor beside him, slumping down into a nearby chair as Elizabeth activated her radio.

"OK, Colonel, go ahead," she said, crossing her fingers inside her coat as she hoped that this latest attempt would work. After giving Sumner a moment to activate the machine, she nodded over at Grodin, who swiftly keyed in the commands that would shut down all power in the city.

For a moment, all was silent in the control room, the entire expedition seemingly holding their breath as they waited for Sumner to let them known that the creature had been contained, until the silence was finally broken with the news that they were safe at last…

A chevron on the Stargate suddenly lit up.

"What?" Elizabeth said, turning to look in the direction of the bright blue light that indicated an active Stargate in this galaxy. "What's happening?"

"I-I don't know…" Grodin said, as he turned to look at the Stargate, which was continuing to dial with no apparent external stimulus. "We don't have any teams off-world, but there's no power currently being sent to the Stargate; somebody dialling in would seem to be the only explanation…"

"Well, _block it_!" McKay yelled, standing up as he looked in frustration at Grodin. "Do you even _realise _what this could do to our plan? If this creature has a choice between the thing that it might recognise as having imprisoned it for the last few thousand years and an active Stargate, what makes you think that it'll stick with the thing that kept it _trapped _for several millennia?"

"I'm _trying_!" Grodin protested, as he reached over to turn the power back on. "If you can do any better, I'd- what the _hell_?"

"Excuse me?" Elizabeth asked, turning to look at Grodin in confusion; so far the man had struck her as being fairly professional- apart from when he punched McKay-, and now he was vocally swearing? "What's wrong?"

"The creature's heading this way!"

"Well, of _course _it is; the power's back on-" McKay began.

"No, you don't understand," Grodin explained, as he loked up at McKay and Elizabeth with an incredulous expression on his face. "There's another active naquadah generator heading this way; _that's _what the creature's following!"

Elizabeth blinked.

"Excuse me; the generator's _heading _this way?" she asked, looking at Grodin in confusion. "As in, it's actually _moving_?"

"Precisely!" Grodin said, indicating his screen in confusion; Elizabeth barely even registered the sound of the Stargate activating behind them in light of this latest revelation. "I can't explain it, but we clearly have an active naquadah generator heading towards us, and the creature's following _it _rather than going after Colonel Sumner!"

"Does this have anything to do with the Stargate dialling like that?" Elizabeth asked, indicating the device in question (She was beginning to doubt that it had ever been an incoming wormhole; if somebody had been attempting to dial Atlantis they would surely have come through by now).

"Well… it's _possible _that the entity could have caused the 'gate to dial by distorting the power systems; proximity to that large an energy source _would _cause Ancient technology to go haywire…" McKay admitted, pausing for a moment before he shook his head. "No, it can't be that; the odds of it dialling a specific address are-"

"Doctor Weir!" one of the other technicians in the control room said, pointing into the main 'gate area. "_Look_!"

As Elizabeth and the rest of the people in the room turned to look at the main area, more than one pair of eyes widened at the sight before them; a tall figure was standing in the middle of the gateroom, clutching an active naquadah generator and dressed in a long dark cloak of some kind. With the lights in the control room already dimmed apart from the candles, the only thing Elizabeth could make out about the figure's appearance- apart from the fact that it was fairly obviously a man- was a faint green glow from his chest, the glow slightly illuminating the silver mask he wore that seemed to cover his face.

"Oh my God…" Elizabeth whispered, recognising the basic details of the mask from all the times she had seen Jinto wearing it while playing. "It's the Phantom…"

"_What_?!" McKay said, spinning around to look at her. "You mean… _that's _the guy Jinto told us told him about this thing? What the hell is he-?"

Before McKay could finish that sentence, the room suddenly seemed to grow even darker as what Elizabeth could only assume was the entity that had been causing them so much trouble appeared from the corridor that the man- the _Phantom_- had just run down. As the staff watched the sight before them, nobody certain what they should do or even if they should do anything, the Phantom slowly edged towards the Stargate, the naquadah generator in his hands as the entity approached him, the creature apparently cautious but nevertheless eager to absorb the energy of the generator before it. For a moment, the scene seemed frozen, the figure of the Phantom standing in front of the Stargate as the dark energy of the creature surrounded the wormhole and the figure standing before it, until it finally completely surrounded the 'gate, concealing the black-clad figure of the Phantom from view.

For a moment, Elizabeth wasn't sure how to feel about what she was seeing; after she'd spent the last week or so since learning about the Phantom's existence curious to learn more about him, seeing him- it could only be him; who else would have worn a mask like that?- apparently sacrifice himself for nothing seemed like such a waste, but she'd still barely even had a chance to get to know him…

Then the dark 'cloud' began to travel through the Stargate, finally vanishing to reveal that the naquadah generator and the figure of the Phantom had also vanished. For a moment, the Stargate remained active, its blue glow illuminating the control room, until it finally vanished, leaving no sign that the creature had ever been present.

After a brief silence, Elizabeth glanced over at Grodin.

"Do… do we know what went through the Stargate before it shut down?" she asked, her fingers crossed inside her coat pocket; for some reason, she strongly didn't want to learn that the Phantom had travelled through the Stargate with that… creature… before she'd even had a chance to meet him (God, what was _wrong _with her; she was acting like some schoolgirl with a crush on a movie star!).

"Well…" Grodin said, studying his laptop briefly before he glanced back up at her, "according to all available readings, apart from a large 'mass' that I'm presuming was the energy creature, the only thing that went through the Stargate was a small object that would appear to be the naquadah generator; if that figure was the 'Phantom' that Jinto told us about, it would appear that he left the room some other way while the entity was travelling through the Stargate."

"In other words, he's still here somewhere?" McKay asked, placing a hand on his forehead and groaning. "_Great_… that's all we need; _another _thing about this city that we don't get."

"Excuse me?" Elizabeth asked, turning to look at McKay inquiringly. "Correct me if I'm wrong, _Doctor_ McKay, but that 'thing' happens to be the man who just saved this city-"

"For reasons that we don't know about and can't be sure will continue to benefit us," a voice said from behind her.

"Colonel Sumner?" Elizabeth said, turning to look at the military head of Atlantis in surprise. "What are you doing here?"

"Sergeant Stackhouse contacted me when the creature began heading this way; with the power having been restored to the tower, I felt that my time would be best served getting back here," Sumner explained briefly, before his expression became more resolute. "As to the presence of this 'Phantom', Doctor Weir, now that we have multiple witnesses of his presence here, I'll be issuing orders to the expedition to alert the security teams to any signs of him, and for him to be captured alive if possible."

"'If possible'?" Elizabeth repeated, staring at Sumner as she tried to conceal her shock. "Colonel, you're talking about the man who potentially just saved our lives-"

"He's a rogue factor in this city, Doctor Weir; just because he helped us out now is no guarantee that he'll continue to help us out in the future," Sumner interjected, his expression clearly resolved on the matter. "If we're going to effectively co-ordinate any kind of offensive action against the Wraith, we can't afford to have a rogue element active; even if this 'Phantom' genuinely does mean well, by staying independent there's always the possibility that he'll jeopardise our own plans of attack by trying to carry out one of his own. I'll make it clear that he's to be taken alive if possible- judging by his actions he clearly knows a great deal about the city that could be of benefit to us-, but beyond that I make no promises if he is discovered."

Clearly noting the uncomfortable expression on Elizabeth's face, Sumner shook his head at her. "Believe me, Doctor Weir, I'm grateful for his assistance in this matter, but the fact remains that we cannot have a rogue element like this 'Phantom' active in this city; the situation is difficult enough without adding in an unknown variable like that."

After staring silently back at Sumner for a few moments, Elizabeth finally nodded.

"Make it clear that they are _not _to hurt the Phantom unless they have to," she said finally. "He saved us all right now; we owe him that much, at least."

"Understood," Sumner replied, nodding briefly back at her before he turned around and headed out of the control room, leaving Elizabeth to turn back and study the control room, unconcerned about the mass of people returning to work behind her.

She understood Sumner's actions, of course- as an independent operative, the Phantom _could _be a problem in their new long-term mission to try and figure out a strategy to oppose the Wraith- but that didn't mean she had to like it.

He'd just managed to save them all, and now they were going to hunt him down like he was an _enemy_?

She _definitely _didn't like this new situation…

And she had no real idea _why _she objected so strongly to it; she didn't even _know _the man she was so desperately wanting to protect!

_What is _wrong _with me_…?

* * *

AN: C'mon, you didn't think I was going to make it _easy _for the Phantom to operate, did you? Just to clarify, I'm not out to portray Sumner as the Atlantis Harry Maybourne, doing what he wants even if it means people get prosecuted simply for trying to do the right thing; I see him as a man who just adheres strongly to the importance of the chain of command and resents somebody who might go against it at a moment's provocation, as opposed to Jack, John and Mitchell, who all acknowledge that there are times when you have to give the chain of command the big middle-digit-up and do what you know is _right _rather than what you're _told _if anyone's going to get out of there alive.

Anyway, hope you enjoy the next chapter, as we explore a bit more of Elizabeth's feelings in the aftermath of this situation, _and _the events of this timeline's 'Thirty-Eight Minutes'…


	7. Silent and Resigned

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

A couple of days later, Doctor Elizabeth Weir sat in her office in Atlantis, her door closed as she stared reflectively at the Ancient shield device in her hands and wondered how she had come to this.

When she'd left Earth, she'd imagined, at best, coming to a city full of living, breathing Ancients who they could talk to and learn first-hand about their culture and technology, and at worst discovering an abandoned Ancient outpost filled with all kinds of advanced technological wonders that they could explore and study at their leisure.

Instead, not only had they landed themselves in the middle of a war against an advanced alien race to whom they were nothing more than a food source, but they had also arrived in a city that was already inhabited by an unknown individual whose origins and motives were a complete mystery to the team…

And the weirdest part was that, even with what she didn't know about him, Elizabeth was already interested in learning more about him as a _person_, rather than the myth that he was to the Athosians.

She couldn't understand what she found so intriguing about him. Admittedly, his reputation as a hero for the Pegasus Galaxy- based on what they'd gathered from the Athosians- was interesting, but, as Colonel Sumner had pointed out, they didn't know his reasons for doing so; for all they knew, the Phantom could be eliminating the Wraith in order to prepare the Pegasus Galaxy for an invasion by the Goa'uld or some other alien race.

Although Elizabeth doubted that the Goa'uld example was the case- from what she'd seen of the Goa'uld during her time as the commander of the SGC and what she'd heard about the Phantom, he was displaying none of the typical Goa'uld ego that would have practically forced them to announce their presence even if they didn't reveal their true natures-, it nevertheless didn't change the fact that the Phantom could have ulterior motives beyond simple heroism.

_So why am I so interested in defending him_? Elizabeth thought, staring reflectively at the shield device that she had found in her office last week. She still hadn't told Colonel Sumner about the device, concerned that he'd confiscate it on the grounds that the Phantom might have tampered with it somehow; for the moment, this was the only tangible proof she had that his 'ulterior motives', if he had any, might actually be beneficial towards them…

No, she had to be honest with herself if she was going to get anywhere; it was the only tangible proof she had that he might care for _her_.

She knew that, when she phrased it like that, it sounded like she was a schoolgirl trying to hang on to proof that the cute guy at the front of the class actually liked her, but it wasn't like that. The shield device simply confirmed that the Phantom _was _thinking of people other than himself; he didn't _need _to give her this shield device, and yet he'd done it anyway…

Despite herself, Elizabeth smiled slightly at her own thoughts.

If anyone else could hear me right now, they'd probably be thinking that the lady doth protest too much, she mused to herself, as she slipped the shield device back into her desk drawer and glanced over at the Stargate a few metres outside her office window. Currently Colonel Sumner and his team were on their first actual mission as a team- it had taken a while for Teyla and the other Athosians to become proficient enough with the Earth expedition's weapons for Sumner to feel comfortable allowing them out on the field with the rest of the expedition-, investigating the planet where the prisoners had been taken earlier in an attempt to find out more information about the Wraith by exploring their base. Admittedly, the task was a risky one- the fact that Sumner's team lacked a qualified pilot was a particular point of concern for Elizabeth; McKay and Sumner had both responded to the ATA gene therapy, but neither of them had trained to fly anything-, but Sergeant Markham had agreed to come along to serve as the gateship's pilot in the event that the main team needed aerial assistance while exploring their surroundings.

Sumner…

Elizabeth groaned inwardly.

Now _there _was a topic she didn't want to get into.

Her military commander may have been good at his job, and at least he respected her authority- he hadn't attempted to replace her as the city's overall commander despite the fact that they were technically in a military situation rather than the simple scientific exploration they'd been expecting-, but at the same time he was a very single minded individual; as far as he was concerned, if you were in Atlantis you had your specific place in the hierarchy and you had to stick to it.

He'd cared enough about the Athosians to try and protect them from the Wraith, true, but if they hadn't been able to offer such valuable insight and information about some of the other natives of the Pegasus Galaxy, Elizabeth had little doubt that he would have been perfectly satisfied simply to leave the Athosians on another planet once they'd identified a suitably Wraith-free location and leave them to fend for themselves afterwards. It wasn't that he didn't _care_, he just preferred to focus on the military side of things and leave Elizabeth to worry about everything else.

It was at times like this, more than ever, that Elizabeth wished she'd been able to bring Colonel Carter and Doctor Jackson along with her; the two of them had proven time and again on SG-1 that they cared about helping people even if Earth wasn't going to get anything out of it, such as when they'd helped to move the Enkarans to another planet when their original home became uninhabitable, or Doctor Jackson's own actions early on in the SGC's existence when he'd allowed the Tollan to go free because he'd felt that getting the advanced technology they possessed wasn't worth the crime that would have been committed to achieve that goal.

It wasn't that she felt that Sumner would do something on that scale, of course, but his automatically treating the Phantom like an enemy hadn't done much to improve her opinion of him...

_Why is it_, Elizabeth mused to herself, _that no matter _what _I end up thinking about since I come here, it always ends up back at the Phantom_?

Seriously, she had to stop doing that; what would Simon think if they ever made contact with Earth and-?

Elizabeth froze.

That was the first time since she'd come to Atlantis that she'd actually thought about Simon. She hadn't forgotten that she had someone back on Earth, of course- the necklace she wore was a daily reminder of him; it was one of the first gifts he'd ever given her-, but with the mystery of the Phantom's existence and motives dominating her thoughts, she just hadn't had the time to reflect much on the life she'd left behind her...

And, now that she was, she found that she didn't really miss it.

More specifically, she found that she didn't really miss _Simon_.

She _had _cared about him, of course, but, looking back at her life with him now, Elizabeth found that she couldn't entirely recall why she'd stayed with him for so long. He'd understood the importance of her work, of course, but he'd never even shown that much of an interest in it; she'd always asked him how his work at the hospital had gone even if at least half of what he talked about would have gone over her head, but he had never once bothered to ask her how her own day had gone. Admittedly, she would have been able to share less about herself with him than he would have been able to tell her- the fact that she spent most of her time on classified projects made it difficult for her to really talk to anyone who didn't have at least Stargate-level clearance or higher-, but she would have at least given him _some _information about her work if he'd only asked.

But he never had.

She had always tried to show an interest in his life even if she wouldn't completely understand it, but he had never _once _asked her to talk about her own life.

Now that Elizabeth thought about it, she wasn't sure what she would have said even if he had asked her. Would she have felt comfortable telling him about the times she'd narrowly averted a potential diplomatic crisis, if not an actual _war_, in the UN? Would she have been able to tell him how she had felt when she was forced to order Colonel O'Neill and his team to go on a potentially suicidal mission to a location that may or not have been the Lost City (Admittedly, it had turned out to not be the actual Lost City, but it had provided them with a ZPM and the coordinates they needed to find the city's 'gate address)? Would she be able to explain why she was so interested in the Phantom-?

Elizabeth could have slapped her head in frustration at herself.

No matter what she tried, it _always _came back to the Phantom in the end.

She just couldn't understand why she was so intrigued by him. Apart from all the tales she'd heard of him from the Athosians, the only thing he'd done that suggested he even _might _have some personal interest in her was the shield device he'd apparently left for her, and even that could be described as potentially stalker-like behaviour rather than him actually being interested in her protection out of the kindness of his heart...

Yet, somehow, Elizabeth didn't believe that.

If he'd just wanted her to trust him, why would he give her something that he couldn't control himself; she'd seen when McKay had been trying to take the shield off that even those expedition members with the most control over the ATA gene had been unable to make the shield device come off before McKay himself had 'decided' to do so.

If he genuinely wanted to harm her, he wouldn't have given her something that she could use to protect herself from him, right...?

_Why is it_, Elizabeth groaned to herself as she slumped into her chair, staring once again at the shield device she held in her hand, _that it's so much easier for me to determine people's potential motives when I'm _not _one of the people who'll be affected by their actions_?

She'd always known what to do when attempting to negotiate peace between countries when the final result would have no impact whatsoever on her and her way of life, but when faced with trying to figure out where she and Simon stood at the moment, she had no real idea where she could even begin...

And as for-

The sound of the Stargate dialling up outside her office broke off that train of thought before it could get much further- a fact that Elizabeth was grateful for; the last thing she wanted was to start debating with herself about the Phantom all over again-, prompting Elizabeth to get to her feet and walk into the control room.

"What's going on?" she asked, glancing anxiously at the technician who was currently sitting at the main control console.

"The reconnaissance team is reporting a medical emergency," the man replied, looking apologetically back at her. "I've alerted Dr. Beckett; he's on his way."

"Put on Colonel Sumner," Elizabeth said, pushing all thoughts of her previous topic of internal debate out of her mind; right now she had more immediate matters to attend to.

"He's the one who's injured," the technician said suddenly, ending any hopes Elizabeth had that whatever the team had encountered was something that could be easily dealt with.

As much as she was uncomfortable around Sumner as a person, Elizabeth was fully aware that he was a very efficient soldier; if he was injured badly enough that he couldn't respond over the radio, then the situation couldn't be encouraging.

"_Flight_!" Lieutenant Ford's voice suddenly said over the radio. "_Gateship One on final approach_!"

Nodding briefly at the technician to activate the radio at their end, Elizabeth stepped forward to respond to the lieutenant's report.

"This is Weir," she said promptly. "What's the nature of Colonel Sumner's injury?"

"_Some sort of funky alien bug attached itself to his neck_," the voice of Lieutenant Ford said over the radio link. "_He's completely immobile_."

"What's it doing to him?" Elizabeth asked, focusing on the central issue of the lieutenant's statement despite the other questions that remained after the lieutenant's statement; there would be time to ask how the bug had attached itself to Sumner's neck later.

"_We don't know_," Ford replied, sounding hurried as he spoke- evidently he just wanted to get the current conversation over with so that they could get back to Atlantis as fast as possible-, "_but we can't get it off him, and we tried everything_."

"You understand the risk of bringing something like that back to Atlantis?" she countered, wishing that she didn't sound like the type of person she'd just been mentally criticising Sumner for being. The fact that she was dealing with an insect of some kind that was almost certainly operating on instinct as opposed to a human being capable of rational thought and decision-making didn't change the fact that she was automatically considering the potential problems rather than the potential benefits; for all she knew this 'bug' could provide them with some important information about how life and evolution in the Pegasus Galaxy had diverged from that in the Milky Way galaxy.

"_Yes, Ma'am, I do, but we really don't have a choice in the matter_," Ford replied briefly.

That last comment was all Elizabeth really needed to know; if Ford, one of the most by-the-book men on Atlantis, thought that there was no other choice but to bring Sumner back in his current condition, then they really didn't have a choice. Ford was one of the more experienced members of the expedition when it came to Stargate travel, having been a member of various SG-teams prior to being permanently assigned to Atlantis; he knew the risks better than most, and, if he believed this was the only option, than it was the only option.

"Understood, Lieutenant," she said finally. "Good luck."

As soon as she had terminated the radio, she glanced over at one of the nearby soldiers and nodded resolutely. "Quarantine the gateship bay."

The soldier simply nodded in response before he left to begin to carry out her orders, accompanied by the technician turning to the consoles before him and quickly beginning to enter the required commands. As she saw the soldiers begin to hurry towards the gateship bay, Elizabeth turned her attention back to the Stargate before her, her fingers crossed as she waited for the gateship to come through and her chief military officer to be back in Beckett's hands (With the situation the way it was, and with Sumner never having managed to get around to appointing a replacement second-in-command, she couldn't afford to lose anyone else).

After a few moments, however, the Stargate remained active without anything having come through it, the alarms simply blaring on in the background with no sign that the cause of them would be arriving any time soon, prompting Elizabeth to glance over at the technician in confusion.

"Where are they?" she asked.

"I don't know," the man replied apologetically. "The gate's still active; all indications read they should be through by now."

Frowning anxiously, Elizabeth turned back to stare at the Stargate, folding her arms as she waited for another few seconds for some sign that the gateship at the other side was going to respond before she finally raised her hand to activate her radio again. "Gateship one, this is Weir, what's your status?"

"_This is Ford; it's good to hear your voice_," the lieutenant promptly said over the radio, which at least assured Weir that the gateship was still intact at the other end of the wormhole even if it wasn't in Atlantis. "_The four of us are still here, but… Markham and Stackhouse… are inside the event horizon_."

Elizabeth's blinked in confusion.

Even with her limited knowledge of how Ancient technology actually worked, she was fairly sure that Stargates weren't meant to get into that kind of situation…

"Say again?" she asked uncertainly, after a brief glance at the current technician assured her that he didn't know how to respond to that statement any more than she did.

"_Ma'am_," Lieutenant Ford's voice continued, "_Gateship One is lodged in the Stargate. Teyla, Dr. McKay and myself are in the rear compartment with the Colonel; he's in bad shape. Markham and Stackhouse are… in the forward section_."

Elizabeth blinked in confusion.

She would be the first to admit that her knowledge of the technical details about how the Stargate worked would always be relatively basic, but she was fairly certain that something couldn't just travel part of the way into the Stargate without

"How did that happen?" she asked.

"_We_ _think_ _it was one of the engine pods_," Ford said after a moment's pause- during which she thought she heard someone else, most likely McKay, say something some distance away from the radio-, "_but there's no way to be sure_."

Going over that statement in her mind, Elizabeth thought that she understood the situation. From what she'd seen of the gateships, they were all equipped with two engines on either side that allowed for greater speed when flying, but automatically retracted whenever the ship was coming through the Stargate and returning to Atlantis. If an engine had been unable to fully retract before entering the Stargate, than the gateship wouldn't quite be able to fit inside the Stargate, and, as a result, the ship would be unable to move past the point where the engines were located…

"If I understand you correctly, you won't be able to access the flight controls?" she asked, clasping her hands together slightly as she spoke, already going over any possible way of dealing with this new dilemma. With the control console inaccessible, they couldn't simply pull out of the Stargate and try to enter the wormhole again, and they had no way of getting the gateship through without retracting the engines…

"Yes, _Elizabeth_," Doctor McKay's voice suddenly said over the radio, breaking her train of thought, "_It's an extremely intriguing conundrum and one that I'd love to discuss with you in detail until this Stargate shuts down and this ship is cut in two_-"

"Rodney," Elizabeth interjected as forcefully as she felt appropriate for the situation, "calm down."

"_At which point of course_-" McKay continued, apparently unaware or unconcerned about her attempts to speak to him.

"Rodney!" she yelled sharply, finally managing to get him to be quiet. "If I'm going to be _any_ help to you at all, I need to catch up!"

Allowing herself a brief pause to make sure McKay had understood what she had just said, Elizabeth began to speak again. "Lieutenant Ford, back it up for me."

After a moment's silence, presumably Ford going over everything before he started speaking, the lieutenant began to talk.

"_We couldn't I.D. the wraith base of operations from space, like we did the last time we were there, so we went to the same landing coordinates as before to get a closer look_," Ford's voice began to say over the radio. "_However, when we arrived at the location it was to discover that the entire base had vanished, leaving only a vast hole that we're assuming, for lack of any evidence to the contrary at the present moment, was the landing site for a Wraith ship; given that they hibernate for centuries, it's plausible that the trees that had been on it when we visited had simply grown there over time. We were forced to retreat after we were confronted by a group of Wraith scouts-_"

"_She hardly meant begin at the _beginning!" McKay's voice suddenly interrupted, the scientist clearly growing frustrated with the lieutenant.

"_This is intel she _needs_ to know_," Ford countered in a patient tone.

"_And we have less than _thirty-eight _minutes-"_ McKay began to say.

"Hold on," Elizabeth asked, interrupting the scientist's yelling before he could go any further. "Why thirty-eight minutes?"

"_Because that's the _maximum_ amount of time a Stargate can remain open in non-relativistic conditions_," McKay answered, sounding particularly frustrated at her attitude, as though he was telling her something that he expected everybody to know. "_It's one of the mo_re immutable _laws of wormhole physics and oh my, look at the time. It's now more like thirty-_five _minutes. Are we all caught up_?"

"I get it," Elizabeth said resolutely. "What do you need?"

"_Help_," McKay replied simply.

"All right," Elizabeth said, pausing briefly to think about her options before she spoke again. "Let me put… Kavanaugh, Grodin and Simpson in a room; see what they come up with."

"_That's good_," McKay replied. "_And the Czech… the Czech… the Czech whose name I can never remember_…"

"Doctor Zelenka?" Elizabeth asked for clarification.

"_That's it_," McKay said in acknowledgement of her statement. "_We'll work it at our end_."

"What else?" Elizabeth asked.

"_We'll call you_," McKay replied briefly. "_Thank you_."

With that, McKay terminated the radio link with Atlantis at his end, leaving Elizabeth standing in the control room just as Doctor Beckett entered the room, swiftly walking over to her with an anxious expression on his face.

"Where's my patient?" he asked.

"There's been a problem," Elizabeth replied briefly, before she placed a hand on the doctor's shoulder to move him along; he may not have any scientific expertise to solve the immediate problem with the gateship, but his medical knowledge could help them find a means of dealing with the problem of Sumner's current 'parasite'. "Conference room."

"Oh no…" Beckett sighed as he walked off, Elizabeth swiftly moving past him to talk to the technician.

"Keep a channel open with them at all times," she said briefly before she walked out of the control room to join the scientists in the conference room. "And turn that damn alarm off!" she called back over her shoulder before she left.

* * *

As Elizabeth began to walk towards the conference room, she was unaware that there was someone else watching the events unfolding in the control room, crouched in his usual place between the 'gate room and the gateship bay (He wondered if Elizabeth would be agreeable towards getting the name changed if he left her a note with his name for them; 'puddle jumper', he felt, showed a lot more imagination than 'Gateship') as he listened in on the conversation via a spare radio he'd taken from a storage room (A small crime, he admitted, but nobody would miss one radio set).

He hated to admit it even to himself, but when he heard the news about Sumner suffering from a medical emergency, a part of him had hoped that it was something a bit worse than an Iratus bug (Lieutenant Ford hadn't named it, of course, but it was the only thing he could think of that might cause a reaction like had been described over the radio). The man meant well, he understood that, but he was so damn paranoid about the motives of anybody who wasn't actively contributing to _his _efforts to defend the city that it was making him very hard to carry out his self-assigned role as the Pegasus Galaxy's guardian…

_Even if it _is _giving me a reason to keep an eye on Elizabeth_… a part of his mind reflected, before he forced it back down into his mind; this was _not_ the time to think about that!

The important thing right now was that the 'gateship' (As they called it) was stuck in the Stargate, the expedition's military leader was dying, and he had just over half an hour before the thing was cut in half as the Stargate shut down.

Even in that scenario, the city would lose at least two people.

He wasn't going to allow that; with the Wraith active and Earth cut off from them due to his own actions- he really needed to see about providing them with the means to crack that code-, the expedition needed every man they could get if they were going to hold the city.

There was only one thing left to do…

Turning away from the sight before him, he began to hurry towards the one room in the city that held the gateship team's only guaranteed way back into Atlantis before time ran out.


	8. No Going Back Now

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

Even as he moved through the tight air ducts and maintenance tunnels of Atlantis- tunnels he'd only ever expected to have to use in the event of a Wraith attack on the city itself; even as he hated how cramped they were, a part of him couldn't help but be grateful that he'd made it a daily part of his training schedule to go through at least one of these things every day to make sure he could use them easily-, the mind behind the silver mask that served as his most distinctive feature for the last decade or so was racing to consider whether his plan would work.

Based on what he'd overheard during the radio conversation between McKay and Elizabeth, it sounded like only the cockpit was actually inside the event horizon, with the door between the forward and aft sections remaining completely outside the Stargate itself. On the encouraging side, that at least meant that if the wormhole shut down before he could manage to try anything, it was still possible that those in the aft section could survive if they kept the door shut until another puddle jumper- McKay and the rest of the expedition members could call them 'gateships' as much as they wanted; to him they would always be puddle jumpers- could get through the Stargate to get them back through to Atlantis.

Of course, how they'd manage to pull that off was a problem; nudging it manually was too uncertain, and rewiring the cloaking device to generate a force field that could be used to _tow _them back would take too long even if somebody here had discovered how to do that before now, particularly he couldn't think of a way to let Elizabeth know about that feature without putting her in an even more awkward position than he already had.

He was grateful that she'd accepted him enough not to let Sumner know about the shield device he'd given her, of course, but he was equally aware that just doing that much had put her in a difficult position; after all, officially she was meant to report any kind of information about him to the military commander to aid in the search for him that was currently taking place.

He was grateful that she hadn't done so, of course, but that still didn't change the fact that she'd put herself at risk simply to help him; he wouldn't- he _couldn't_- do anything else that might jeopardise her position.

No, with no other means of helping the expedition without actually going up to a scientist and telling them what to do face-to-face, he was going to have to simply take a chance and hope that the mental picture he'd created of the jumper's current situation- more specifically, the idea that only the _front _part of the engines had managed to get into the event horizon- was accurate.

If the jumper was too far into the wormhole, this plan was _never _going to work, and all he'd have accomplished for this effort would be sore elbows and leaving him in a position where it would be relatively easy to capture him…

* * *

As Elizabeth walked rapidly into the conference room, she looked resolutely around at the scientists who had already gathered together. If nothing else, she had to admire their dedication; they'd been in this city for barely a couple of weeks yet and already the scientists knew the best routes to get from one point to another at short notice.

"All right," she said, looking around the room as she spoke to make sure everyone was present; she'd been occupied with making sure that there was nothing the technicians could do at their end to help the group, and so hadn't had the opportunity to make a head count. "You've all been briefed; we have less than half an hour."

Having finished her brief glance, she raised a curious eyebrow at the absence of one of the staff. "Where's Doctor Zelenka?"

"He's working up a simulation in Gateship Two; he went straight there," one of the scientists- Kavanagh, Elizabeth recalled his name was; she still had a little trouble matching the names on her various reports with the faces she saw in the corridors- said.

"That's good," she said, allowing herself a brief moment of satisfaction at the knowledge that one of

"If there was _time_, it would be," Kavanagh interjected, sounding briefly frustrated even as he turned his attention back to the papers that he currently held in his hands; Elizabeth briefly noted that they contained what diagrams the expedition had been able to make of the gateships during their admittedly limited opportunities to examine them up to this point (Nobody was particularly eager to risk doing anything to such fascinating pieces of technology until they were certain that they knew what they were doing, so research had been limited to avoid accidentally causing long-term damage to the ships).

For a moment, Elizabeth simply stood in silence as she glared at Kavanagh, making her disdain for the implications of his last statement clear before she finally spoke.

"Let's not admit defeat just _yet_, Doctor; there are six people on that ship," she informed him coldly, ignoring his annoyed expression as she turned around to look at the rest of the gathered scientists in case they had any further suggestions to offer.

"I'm just the medical doctor here, so forgive me if this is a stupid question," Beckett's voice suddenly broke in from off to the side. "If they just stepped through the event horizon, wouldn't they come through the front part of the ship when the gate shuts down?"

"The front half won't rematerialize on this side," Kavanagh promptly responded (Normally Elizabeth would have commended his prompt assessment of the situation, but the fact that he'd started speaking almost as soon as Beckett had finished his sentence limited any potential pride in his actions; for all that Kavanagh could have known Beckett might have still wanted to say something).

"The Stargate transmits matter in discrete units," Grodin continued (Elizabeth noted, much to her approval, that he at least gave Kavanagh a moment to continue if he had anything else to say before speaking himself. "The front half of the ship cannot re-materialize until the whole ship has crossed into the event horizon. The Stargate is essentially waiting for the contiguous components- meaning the gateship _and_ everyone inside- to enter completely before it can transport them."

For a moment, Beckett simply stared at Grodin, before he turned his attention to look inquiringly at Elizabeth.

"He says the gate only sends things through in one piece," she clarified.

"Right," Beckett said, sounding like he wished he had never spoken in the first place. "Sorry."

"Unfortunately," Grodin continued as he turned to face her, drawing her attention back to the matter at hand- normally Elizabeth would have apologized to Beckett for the rather abrupt dismissal, but the current situation was their more immediate problem right now-, "the outgoing Stargate won't transmit the matter stream until the demolecularization is complete. When it shuts down, the entire forward section- along with the men inside- will cease to exist."

"And what about the others?" Elizabeth asked, already knowing that she wouldn't like the answer she was about to receive.

"The ship will be severed instantaneously along the event horizon," Grodin said, his expression grim as he delivered the news Elizabeth had been hoping not to hear. "They'll be exposed to hard vacuum… in twenty-nine minutes."

For a moment, there was silence as Elizabeth and the rest of the room grimly contemplated the fate that awaited Atlantis's military commander and his team, before Doctor Simpson- one of the younger female scientists- spoke up.

"What if they closed the bulkhead door?" she asked, indicating the feature in question on a gateship diagram in front of her.

Elizabeth could have kicked herself for not thinking of that solution herself; it was so _obvious_…

"The rear portion of the ship would remain pressurized; become a sort of lifeboat," she said, looking at the younger woman with an approving smile.

"It will leak atmosphere like a sieve," the man who was rapidly becoming her unofficial assistant countered from behind her, his tone making it clear that he doubted the reliability of that last suggestion.

"It could buy enough time to send a second gateship-," Simpson continued.

"And do what?" Kavanagh interjected.

"Figure it out," Weir said briefly, cutting off any further argument as she glared momentarily at Kavanagh before she turned to look at Grodin. "Contact gateship one and make the recommendation."

"Yes, Doctor," Grodin said, standing up and heading over to the control room.

"Keep brainstorming down here," Elizabeth continued, turning to look at the rest of the room as she indicated the door behind her. "I'm going to see if Doctor Zelenka's managed to come up with anything yet."

After receiving confirming nods from the rest of the staff, Elizabeth stood up and walked out of the conference, quickly heading for the stairs that led to the gateship bay. Having arrived in the gateship bay, she glanced around the room for a moment before she identified the illuminated form of Gateship Two, currently rotated in the hanger so that the exit hatch was facing inwards rather than the cockpit. A quick glance inside the ship was all that she needed to confirm that Zelenka was there, studying some of the control crystals located in the roof of the back section of the ship while a couple of the other scientists took notes on a laptop and studied the walls for anything else that they could use.

"_Můžeš mi dát ty nejnovější data, prosim_?" Elizabeth heard Zelenka's voice say as she approached the ship."_Já se s tímhle nemůžu hnout._"

Quickly going over that sentence in her head- Czech, unfortunately, wasn't one of the languages she knew, but she'd gathered enough about it to understand the basics at least-, Elizabeth gathered that Zelenka was still having some problems processing all the data that he and the team had uncovered so far, but she took some comfort in the knowledge that he was at least making an effort.

"Doctor Zelenka?" she asked as she entered the gateship, prompting the Czech scientist to briefly glance down in her direction before he returned his attention to the matter at hand.

"Apologies for not attending your briefing, Dr Weir; there was no time," he said briskly, pausing in his work to make a few notes on the electronic pad he held in his hands.

"I don't want to slow you down," Elizabeth said, as she walked around Zelenka to better watch him as she spoke, "but I need to know what you're working on so I can communicate it to the team on Gateship one."

"We are," Zelenka replied, his attention still focused on the panel before him even as he spoke to her, "attempting to retract the., um…the, er… the gt… the drive pod back into the fuselage, from _inside_ the rear compartment."

"Anything yet?" she asked hopefully, aware even as she spoke that it was a fairly pointless question; if there had been any such discoveries made he would have told her about them already.

"Well," the Czech said, clearly wanting to give her something even as he continued to study the machinery before him, "there is much redundancy in Ancient technology, making it dangerous for them to experiment with it in this way…"

"So they might accidentally open the rear hatch or shut life support off entirely?" Elizabeth asked, wanting to make sure that she understood the risks of the current situation before she returned to the other scientists; right now, with her traditional field of expertise relatively useless in solving the current crisis, anything she could bring to the table would feel good right now.

"Yes, yes, yes, yes, which is why we are attempting to isolate the correct control pathway," Zelenka relied, tapping at one of the crystals before him with his tool before he noted the results on his pad.

"Understood," she replied, nodding slightly at him. "What could I do to help?"

"Stop talking, please," the Czech scientist replied briskly, even as the slight smile that accompanied those words significantly detracted from what could otherwise have been a harsh statement. As he turned his attention back to the panel, Elizabeth simply shrugged and walked away from the gateship; the sooner Doctor Zelenka could get back to focusing on the matter at hand, the more likely it was that he'd find a solution to get the gateship back to Atlantis before it was cut in half.

Right now, the best thing that she could do would be to get back to the conference room and see if anyone there had managed to come up with anything during her absence.

* * *

Down in the room that housed the main control chair of Atlantis, the single Marine currently on guard duty- ever since the Phantom's presence had been confirmed, Sumner had insisted that vital areas of the city receive at least a basic measure of protection to prevent the man from trying anything- never noticed the silent figure that crept up from behind him, dressed all in black, before the new arrival struck the marine on the back of the neck and sent him into unconsciousness.

Looking down at the figure currently sprawled on the ground before him, he couldn't help but wish that this kind of measure hadn't been necessary; it was going to create even more difficulties for him in the future if he started attacking members of the expedition just to achieve his own goals, even if they benefited the expedition itself…

But, at the same time, he knew that he'd had to do it. He was well aware that there might be some people among the expedition who didn't share Colonel Sumner's belief that he needed to be captured in case his continued independent status unintentionally jeopardised the expedition's own plans, but he couldn't take the chance that this man was one of them. If he wasn't able to gain access to the control chair, than what might be the gateship team's last chance to get back alive would be lost before it had even been attempted, and with only- he glanced at the watch of the man lying before him- approximately twenty-eight minutes left before the Stargate automatically shut down, he didn't have the time to try and convince the marine to let him try it.

Call him impatient, but he'd rather _not _wait until the last minute to try and get the gateship through the Stargate…

Even as he began to move towards the control chair, however, he raised one hand to the ear holding his 'acquired' (It wasn't stolen; nobody had been using it when he'd taken it, so how could it be stolen?) radio and turned it on, the radio automatically tuning in to the radio link currently open between the gateship and the control room; if he was going to guide the gateship through, he was going to at least get an idea of the situation at the other end before he tried anything.

"-_did it attach itself_?" Doctor Beckett's voice said over the line; instinctively he lowered his breathing and tried his best to remain silent, recalling past experiences when he'd been temporarily trapped on board Wraith hive ships and stealth had been a requirement of his long-term survival.

"_Well_…" Sumner's voice replied weakly- evidently the Iratus bug was really starting to get to him-, "_we were on our way back to the gateship, with the Wraith shooting at us… I told the others to get moving while I bought them time_…"

For a moment, as Sumner continued speaking he tuned out the other man's voice, preferring to think more about what he'd just heard; he couldn't do anything to directly help with the central problem of getting the bug off Sumner's neck without risking capture at least, and the medical side of things was never his strong point anyway.

Besides, right now he had a more immediate question to answer; what would a Wraith patrol be doing on a planet that they'd have presumably abandoned as soon as they'd confirmed that the hive ship's presence there had been compromised? Even if the Wraith were aware that the Expedition weren't actual Ancients, they would at least know that another Ancient-technology-controlling power had entered the Pegasus galaxy, and, with them now aware that the location of at least one hive-ship had been compromised, they wouldn't want to stick around if they could help it.

It was one of the main reasons why he'd only managed to take out around five hive-ships over the last decade or so; although his recon missions provided him with everything he needed to know about the ship's weaknesses, he always had to be sure to strike the ship in such a manner as to eliminate the Keeper and the ship practically simultaneously, or at least to do enough damage to the ship to prevent the Wraith's psychic network 'transmitting' the news of the attack and prompting the rest of the ships to activate…

And he was getting off-topic right now; the reasons why he hadn't managed to destroy more hive-ships weren't important. What _was _important was figuring out how the Wraith had _known _that the team were on the planet at that point- and they had to have known the team were there; there was no other way to account for the presence of a Wraith team on a planet that clearly lacked for any other form of life that the Wraith could use for food- and, with that knowledge, working out a means to prevent it from happening again…

Even as he settled into the control chair, keeping it on standby until he was ready to use it- there was no sense in tipping the expedition off to his presence until he was ready to do what he had to do-, his mind was rapidly racing through all the possible explanations for what might have happened to draw the Wraith to that planet at that time.

* * *

As Elizabeth walked past the control room, she barely even registered Beckett's attempts to figure out a means of dealing with the insect that was currently strapped to Colonel Sumner's neck; as with Zelenka, there was nothing she could usefully contribute to that particular problem, so she might as well return to the conference room where she might at least be able to help out in a co-ordinating manner if nothing else.

"If you activate the field, they'll die!" she heard Simpson say as she approached the conference room; it sounded like her role as negotiator was indeed going to be required here after all.

"Hey, we can always open it again!" Kavanagh's voice countered. "If they fix the problem-"

"But they may not have time!" Simpson countered.

"If they don't we could destroy this facility!" Kavanagh retorted, just as Elizabeth entered the room in time to see the two scientists standing on either side of the table glaring at each other.

"Well, I do-!" Simpson began.

"You're supposed to be working on _solutions_!" Elizabeth yelled, simultaneously cutting the argument short and making certain that the rest of the room knew that she was back.

For a moment there was silence in the conference room, Kavanagh looking frustrated while Simpson simply lowered her eyes, evidently at least slightly embarrassed about her loss of temper, before Kavanagh broke the silence.

"We think the gateship must be damaged for this to have happened in the first place," he said, looking at Simpson in what Elizabeth felt was a rather pointed manner as he continued. "Ancient systems are too advanced for this to have been _pilot_ error."

"So?" Elizabeth asked, deciding to ignore the glare that had just passed between the two scientists. As far as she was concerned, if they had differing opinions on what had caused the accident, that was their problem; all that mattered to her was if they could figure out a solution.

"So," Kavanagh continued, "depending on the extent of the damage, we can't rule out a catastrophic power feedback in the drive manifold-!"

"Without the technobabble, please," Elizabeth countered, her hands behind her back as she looked pointedly at Kavanagh.

Fortunately for Kavanagh- if he'd continued talking for much longer Elizabeth had a feeling she would have tempted to hit him- it was Simpson who decided to continue the explanation. "Doctor Kavanagh was pointing out that there is a _very slim chance_ that with the cockpit controls interrupted and the pod damaged, the main drive could overload-"

"She means to say explode," Kavanagh interjected, glaring briefly at Simpson before he turned back to look at Elizabeth. "Especially if McKay starts nosing around inside the control conduits to retract the drive pod manually, and he _will_; I know I would!"

"Zelenka is working on simulations," Elizabeth countered, hoping that the knowledge that they were already trying to prevent that from happening would make Kavanagh calm down. "I just came from there-"

"If there is a catastrophic overload," Kavanagh countered, clearly dissatisfied with her attempts at assurance, "the full force of the explosion will break up the gateship, follow the burning fragments through the Stargate like a _bomb_."

After staring silently at Kavanagh for a moment to better determine his belief in what he was saying, Elizabeth nodded in understanding; even if she didn't totally follow the technical details, she could appreciate that Kavanagh genuinely believed what he was saying.

"You think the risk of this happening is minimal?" she asked Simpson, turning to look at the younger woman.

"In my opinion?" Simpson replied, as she stood up slightly to glare at Kavanagh as he sat before her. "Yes."

"You all agree?" Elizabeth addressed the other scientists, not surprised when they all nodded in agreement; Kavanagh's abilities were good, but she recalled from his file that he had a tendency to always assume the worst, particularly in situations where he himself might have been in danger. "Then we take the chance."

"I thought it was important to point out the risk-" Kavanagh elaborated, as he stood up and crossed his arms.

"Fine," Elizabeth interrupted, unwilling to hear his attempts at justification. "You did. Now please, worry a little bit more about their lives and _less_ about your own ass."

Ignoring his disdaining look in her direction, Elizabeth turned to look back at the rest of the scientists after a brief glance at her watch.

"Twenty-three minutes," she said simply as she walked out, leaving the scientists to turn their attention back to the papers laid out before them.


	9. Mystery of Soprano's Flight

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

As he lay on the chair, simultaneously taking the opportunity to relax while making sure his mind didn't relax so much that he triggered the chair by accident, he took care to pay close attention to the situation currently being discussed between the puddle jumper and Beckett's medical team; after spending so long essentially 'winging it' when it came to medical matters, it was almost refreshing to have access to a person with more professional training.

Lieutenant Ford and Teyla Emmagan- nice woman, really; he had a feeling that they would have gotten along well if they ever had the chance to talk face-to-face- had just finished going over everything that was currently available in the 'gateship's' (Seriously, how unoriginal could you get; at least when he'd come up with 'puddle jumper' he'd actually put a bit more thought into the naming process) medical inventory when another, far more voice suddenly cut in over the radio link.

"_Gateship One, this is Weir_," Elizabeth's voice said, bringing a brief smile to his lips; even in the middle of a crisis like this, she still managed to sound in control. "_Doctor Zelenka's come up with something_."

"_He's positively identified the control systems on the _port side of the gateship that retract the drive pods," Doctor Grodin added (He thought he heard McKay mutter something on the other end, but evidently it wasn't that important). "_I'm relaying the schematics to your datapad_."

"_Thank you_," McKay replied briefly at the other end. "Now _we're getting somewhere_."

"_What_?" Lieutenant Ford's voice said, slightly less audible than McKay's; he'd be prepared to bet at least one of their naquadah generators- those things were excellent; anything that would leave the ZPM with more power when they'd really need it couldn't fail to be a good thing- that neither man knew they could still be heard.

"_Zelenka's identified the control pathways to the engine pod_," McKay explained, the faint sound of activity as he spoke suggesting that he was lowering the control panel in question even as he spoke, "_which means that's increasing my chances of fixing this from one in a_ million _to one in a_ thousand_, but, uh…it's something. Elizabeth_?"

"_Yes_?" Elizabeth's voice replied, even as the man in the chair crossed his fingers; maybe they'd manage to get the thing through now and he wouldn't _need _to resort to his slightly riskier plan (Not that it would do him much good in terms of his standing with the expedition, of course; even if he didn't do anything right now he still wouldn't be able to get around the fact that he'd knocked one of their number out, whatever his motives for doing so were).

"_I'll only have seven to nine seconds to warn you if I accidentally trigger a catastrophic overload_," McKay replied, instantly prompting the listener to re-evaluate his opinion of the plan- it was, if anything, _less _safe than his; at least his wouldn't cause anything to actually _explode _if it went wrong-, "_so if I tell you to raise the shields… don't hesitate_."

"_We're aware of the risk, Rodney_," Elizabeth replied, her voice calm despite the potential danger that could result from what she'd just heard. "_Do your best_."

For a moment, there was silence on both ends, the Atlantis staff presumably waiting for news of the situation in the gateship while the gateship team prepared to do the work in question, until Lieutenant Ford's voice broke the silence once again.

"_We're starting with iodine_," he said briefly, followed by a brief pause before he spoke again. "_Scratch iodine_."

"_What else have you got there_?" Beckett's voice asked.

There a brief moment of muffled conversation on the gateship end of the line- it sounded like McKay was asking for something; most likely food, given what he'd gathered about that man's habits over the last couple of weeks-, and then Ford spoke again.

"_We're going to try alcohol now_," the young lieutenant said.

"_Place a few drops on the soft tissue to see how it reacts_," Beckett said.

After another few brief moments of muffled conversation at the other end, Ford spoke again. "_No reaction to alcohol_."

"_Right_," Beckett said on the other end, in a brisk voice that made it clear he had decided to simply acknowledge that failure and move on to another possibility. "_What next_?"

After some muffled comments from over the radio, Ford's voice was heard once again as he muttered something about water that couldn't quite be heard, only to be followed by his voice suddenly yelling "_Sir! Sir, are you all right? Sir? Colonel_?"

As Sumner's voice suddenly roared in pain over the communication link, all he could think of was that he hoped the man's current pain wasn't as bad as it sounded at present, and that Sumner would be spared from it sooner rather than later.

_Come on_… he growled, gritting his teeth as he glanced at the watch of the man lying before him; they were down to just over ten minutes before the wormhole shut down on them and that damn bug _still _wasn't off. If they took much longer than this to sort the problem out, he was going to just hang the risk and

"_Sir, are you all right_?" Ford's voice continued to say over the radio, drawing his attention back to the matter at hand. "_Sir? Colonel? Colonel? What's happening_?"

The sudden sound of someone- judging by the brief yell he heard it definitely wasn't an inanimate object- being thrown at something else was nearly enough to make him forget himself and get the ship moving, but he stopped himself in time; he still had no idea what would happen to the Iratus bug if it went through the wormhole, and they still had a decent amount of time before the Stargate reached the moment when it would _have _to shut down.

"_What's happening_?" Elizabeth's voice said, the concern in her voice prompting a brief spike of jealousy before he got it under control; the last thing he wanted was to lose focus while he was in the chair.

"_It reacted to either the salt or the water_," Ford replied promptly.

"_Or the combination of both_," Beckett said, clearly trying to think of what to do even as he spoke. "_Did it loosen its hold on Colonel Sumner_?"

"_Negative_," Ford replied apologetically.

"_If anything, it dug in more_," Teyla put in, her voice clearly reflecting her frustration at the current crisis.

"_Most likely a primitive defensive reflex to salt water_," Beckett speculated, only to be greeted with muffled responses as further conversation took place between the small group trapped in the gateship.

For a moment, the only sounds audible through the radio link were faint sounds of conversation, clearly taking place a short distance away from the radio itself, until Elizabeth's voice broke through the silence.

"_Ford, what can you tell me_?" she asked.

"_The gateship has shifted slightly_," Ford replied, his tone grim as he spoke. "_The rear compartment has now breached the event horizon. Dr. McKay…_"

He paused, most likely looking at the scientist in question for confirmation of what he was about to say, before he continued speaking. "_Dr. McKay… is still hopeful he can retract the drive pod in time_."

"_Understood_," Elizabeth's voice said. "_We haven't come up with anything yet, but there's still time_."

"_Yes, Ma'am_," Ford replied briefly; evidently the classic military man, he seemed to prefer confirming others' opinions when he couldn't come up with anything to say about the situation himself.

"_How is Colonel Sumner_?" Elizabeth asked, evidently wanting to focus more on something where she felt at least slightly more in control than on the technical details.

"_I'm still here_," Sumner grunted, evidently still in pain from the Iratus bug as it sucked away at his life force.

"_Hang in there, Colonel_," Elizabeth said simply. "_We're working on the problem_."

"_I gathered as much_," Sumner replied grimly, even as he clearly didn't believe they'd manage to accomplish anything. "_I should have known that thing wouldn't have let me go if he thought I could live…_"

"_What thing_?" Elizabeth asked.

"_The wraith_," Sumner replied grimly. "_One of them found me shortly after the bug first attached itself, but… damn thing just looked at me and left… probably because he knew I was as good as dead anyway…_"

"_You are_ not _going to die on us now, Colonel_," Elizabeth stated decisively (Even as illogical as he knew it was, a part of him couldn't help a faint twinge of jealousy; even with all the hostility between Elizabeth and Sumner, she was still so determined for him not to die).

"_We should send him through the event horizon_," Ford put in. "_If Dr. McKay figures it out in time, we can fix the Colonel up on the other side, and if he doesn't, we're all dead anyway_."

"_So, no pressure_?" McKay countered, clearly not in favour of the added pressure being placed on him at a time like this.

"_Colonel Sumner_ would_ effectively be in suspended animation for the entire time_," Grodin's voice added.

"_We can't risk that_," Beckett interjected.

"_Why not_?" Ford asked.

"_If the creature reacted that violently to a few drops of water, who knows how it would react to Stargate travel_?" Beckett pointed out.

For a moment, the listener was almost tempted to thank Beckett profusely for voicing the reason he'd not done anything yet himself. He was fairly confident that he could get the 'gateship' through the Stargate so long as it wasn't too far into the event horizon, but as long as that Iratus bug was attached to the colonel, he had no desire to find out the hard way what effects Stargate travel would have on that thing; he'd seen someone try to escape through a Stargate while a Wraith was feeding on him once, and the results at the other side had been less than pleasant.

"_You're telling me Colonel Sumner can't come through the gate while that thing is on him_?" Elizabeth's voice said over the radio, cutting off his train of thought.

"_Then we must do something now_!" Teyla responded, her voice continuing to reflect

"_Hit me with the defibrillator_," Sumner said grimly.

For a moment there was silence as everyone took in the fact that the expedition's military commander had essentially just asked to be euthanised- the man in the chair in particular hadn't thought of Sumner as the type to ake the easy option out unless there was no other choice, and the bug definitely had a long way to go before it was finished with him-, but then Doctor Beckett's voice broke the silence.

"_You may be on to something, Colonel_," he said, actually sounding enthusiastic for the first time since this situation had begun.

"_You said that might _kill_ him_!" Ford protested.

"_That's the idea_," Sumner responded grimly.

"_I don't understand_," Teyla's voice interjected, sounding ever more confused at her new allies' reactions to the idea of someone essentially killing themselves.

"_Teyla_," Beckett began, clearly taking it upon himself to provide the explanation, "_you said this creature is like a Wraith_?"

"_Yes_?" Teyla replied, her voice still reflecting her confusion at the apparent rapid change of topics.

"_Then how do you think it would respond if, God forbid, Colonel Sumner were to die right now, then_?"

After a brief silence as she contemplated what she had just heard, Teyla spoke again.

"_It would stop feeding_," she said, clearly realising what the doctor was saying even if she didn't like it.

"_Exactly, just as a Wraith would_," Beckett clarified, evident excitement at the possibility in his voice.

"_How is that an idea_?" Elizabeth asked (Not that he could blame her for not seeing it, of course; it wasn't in her mentality to try and stop death by _causing _it).

"_We're suggesting that we fool the creature into thinking its prey is dead by stopping the Colonel's heart_," Beckett explained. "_If I'm right, it should let him go_."

"_So when the thing lets go, we give him another jolt_?" Ford said.

"You could give that a try," Beckett confirmed. "_If it doesn't work, send him through the event horizon; he'll keep there as good as a deep freeze_."

"_Colonel Sumner_," Elizabeth cut in, clearly anxious about the implications of what they were about to do, "_are you sure you want to do this_?"

"_I want this thing off_," Sumner replied grimly.

For a moment Beckett's voice faded- presumably addressing somebody else at his end of the radio- before he spoke again. "_Lieutenant Ford, do you know how to do this_?"

"Yes, Sir," the lieutenant said briefly, before he terminated the radio connection. For a few moments, there was nothing but silence over the radio, the gateship's end of the line no longer transmitting as those on the Atlantis side waited anxiously for news on the fate of the expedition's military commander, until, after a couple of minutes had passed, Lieutenant Ford's voice finally spoke again.

"_This is Lieutenant Ford_," the young marine's voice said, remaining calm despite the dire news that he was now relaying to the rest of the expedition. "_The creature's successfully been removed from Colonel Sumner, but we were unable to revive him. Both he and Teyla are now on the other side of the event horizon_."

As soon as his brain had finished processing the sentence, he knew that this was his moment to act.

With the bug eliminated and Sumner as safe as he was going to get, now was as good a time as any to carry out his plan. If he recalled his medical knowledge correctly, right now, with the medical team hopefully still waiting in the gateship bay, given how long it must have been between them 'killing' Sumner and Ford's subsequent message- allowing for time to make any final preparations such as cutting his shirt open to apply the defibrillator-, there'd only be something like a minute for them to get Sumner breathing again if they wanted to avoid him suffering from brain damage due to prolonged oxygen deprivation.

It was now or never; even if this worked, Sumner was going to be cutting it _really _close on the other side.

He just had to hope that his old attempts to practice this 'trick' had paid off as well as he'd felt they had at the time.

Reaching out with his mind to 'feel' the puddle jumper on the other side, he smiled slightly as he sensed the drones on either side; just as he'd hoped, the ship _wasn't _far enough into the event horizon for his access to them to be totally cut off.

_Here goes nothing_… he mused.

* * *

"_Thank you, Lieutenant_," Doctor Weir's voice said over the radio (Doctor McKay just wished she had something else to offer them other than these little pleasantries; they helped to keep spirits up, but there were only so many times polite encouragement could help you when you were in this kind of mood)). "_Rodney, you have seven_-"

Before he could even hear the end of the sentence, Rodney McKay was shocked to feel the gateship actually move _backwards_ a few feet, exposing what looked like Teyla and Sumner's legs on the other end of the event horizon currently visible through the open door without actually returning them to real time.

"What the…?" Ford asked, looking in confusion over at the astrophysicist. "Did you do something?"

"Oh yeah, my artificially created Ancient gene suddenly got boosted to allow me to control this thing _without_ the need for the controls!" Rodney yelled in frustration at the lieutenant. "Seriously, _nobody's _Ancient gene is that advanced; not even the _natural _genes are good enough to pull off something like that! Besides, don't you think that-"

Before Rodney could say anything more, he heard the faint sound of the ship's exterior engines shifting position outside the ship- he didn't hear the clunk that signified that they'd fully retracted, but they definitely weren't in the same position they'd been in when they'd first gotten stuck in the 'gate originally; what was that all about?-, only for the event horizon before them to sudden move rapidly towards them…

* * *

Even as she stood in the control room anxiously looking at the wormhole before her, Elizabeth still doubted she'd ever be able to fully understand what was taking place before her. One minute, and her staff were in the conference room, anxiously going over every possible solution for the gateship's current crisis that they could think of- the most outlandish suggestion so far was trying to find an Ancient teleportation device to send another gateship along; even if the Ancients had mastered that kind of technology how would they be able to learn how to use it in under five minutes?-, the next minute she was hearing Grodin's shocked voice yelling at her from the control room. Hurrying through to the source of the calls, she and her team were shocked to witness something that none of them had thought possible; right there, in front of their eyes, the gateship was coming through the Stargate.

"What the _hell_?" Elizabeth said, looking over at Grodin in confusion. "How's-?"

"I don't know; Doctor McKay gave no indication that he had come up with anything at that end!" Grodin said, looking back at her in evident frustration as the gateship continued to advance. "It's as though-"

"Wait a minute…" Kavanagh said, his eyes widening behind his glasses as he looked at the ship before them, its engines now protruding from the wormhole; Elizabeth was surprised to note that they were still extended, but were no longer at the full length she'd seen demonstrated in the docking bay on occasion. "Didn't Colonel Sumner say that these ships were equipped with drone weapons like the type that was found in Antarctica?"

"Yes; why?" Elizabeth asked, looking over inquiringly at Kavanagh.

"Well, look at the drive pods," Kavanagh said, indicating the engines on either side of the gateship as they prepared to retract. "Doesn't that glow they're letting off look like the one generated by the drones?"

Elizabeth blinked.

Now that she thought about it, the faint golden glow visible from around the gateship's engines _did _look rather like the glow that had been generated by the drone weapon she'd seen in action when Carson had accidentally activated it after sitting in the Antarctic control chair…

_But how could _that _make sense_? she asked herself, still looking in confusion at the ship before her ascended up towards the gateship bay (She didn't follow it, of course; she could contribute nothing by being up there and might even just get in the way while Carson attempted to revive Colonel Sumner). _What could cause the gateship's _drone weapons _to turn on like that?_

It would appear that they had just discovered another mystery about the city that they'd need to solve...

Elizabeth wasn't sure whether to enjoy these little puzzles or get frustrated about them by this point.

* * *

Later that night, as Teyla Emmagan lay in her bed, she couldn't help but find herself reflecting on the day's events now that the danger had passed and Colonel Sumner was out of danger. The insect that had attacked him was currently in Doctor Beckett's laboratory undergoing an in-depth examination under controlled conditions; given its apparent similarity to the Wraith, nobody was willing to take any chances that it might possess at least some degree of their regenerative abilities.

In general, although the situation had been resolved with (From what she gathered; she naturally had no way of knowing how much time had really passed between her entering the event horizon with Sumner and their subsequent return to Atlantis, even if she believed McKay when he only a few seconds had passed) at least five minutes to spare, it still left them with a great deal of unanswered questions about what had actually taken place at the resolution of the crisis.

According to what McKay and some of the other scientists had told them in the subsequent briefing after Colonel Sumner had been revived, someone had apparently broken into the room holding the control chair of Atlantis- apparently a chair where one person would be capable of controlling the city's entire defence in the event of an attack by other ships- and, having knocked out the person guarding the chair at the time- a Sergeant Bates, if she recalled correctly-, had proceeded to use the chair to take control of the gateship's drone weapons. With the drones providing the ship with motion in the absence of the control room, and thus allowing the gateship to move once again, the gateship had been moved back slightly to 'dislodge' it from where it had been previously trapped, and the positioning of the drive pods had subsequently been altered before giving it the necessary push forward to allow it through the Stargate, thus leaving the drones free to provide energy to push the ship through the wormhole despite the relative lack of forward momentum.

While the technical aspects of the discussion had eluded Teyla to a certain extent, she had nevertheless understood enough to determine that none of the Atlantis expedition had any idea of who had actually used the control chair in that manner; very few of the people from Earth possessed the ability to control the machinery left by the Ancestors well enough to accomplish that goal, but at the same time there was no other explanation for how the ship had come through the Stargate without any action on Doctor McKay's part save that somebody had done it deliberately from this end.

Of course, Teyla was fairly certain that all of them knew who had been behind their recent rescue- his actions after Jinto had released the shadow creature a mere few days ago were evidence enough for her that he was resolved to act in their benefit- but given Colonel Sumner's attitude towards the man in question, she, for one, was reluctant to say it and cause him further problems.

She understood why he remained in the shadows, of course- Colonel Sumner was a good man, but his belief in his 'chain of command' left him with a very narrow-minded viewpoint when it came to any independent figures inside 'his' city-, but when she considered everything that the… individual (She somehow could not think of him as a man after all that he had done over the years)… might have to teach them…

A slight sound, as though that of a foot touching the ground, broke off Teyla's train of thought.

_Someone was in her room_…

Sitting up sharply, she waved a hand at the device that apparently controlled the lighting in her room, only to find herself staring in shock as the light gleamed off the silver mask of the black-clad figure standing before her.

"_Phantom_…" she whispered, unable to stop the almost reverential tone that crept into her voice as she stared at the figure standing in front of her, a slight smile on his face as he looked at her.

After hearing of his legend for more than a decade- almost her entire adult life-, to actually be in the presence of the one man whom almost the entire galaxy owed a debt to for his actions in defending them against the Wraith…

Teyla would be lying if she didn't admit that the situation was almost overwhelming

What she didn't understand was what he was _doing _here.

* * *

AN: Any guesses? C'mon, you know you want to…


	10. Catch Them With Their Magical Lasso

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

The next morning, Doctor McKay came down to his laboratory, only to find Teyla standing in the middle of the room, looking anxiously at him with a metal object that McKay recognised as her necklace clutched in her hand.

"Teyla?" he asked, looking in confusion at the Athosian woman before him. "W-what are you doing here?"

"I… wished to talk with you about… recent events," Teyla replied, looking calmly back at the scientist as she spoke.

"Really?" McKay replied, his confusion slightly abating as he sat down at a nearby desk, indicating a chair just opposite him where Teyla could sit herself. "What about recent events?"

"The presence of the Phantom in Atlantis, for one thing," Teyla answered, as she sat opposite him.

Rodney blinked.

"The Phantom?" he repeated, surprise now his dominant emotion as he looked back at Teyla. "What do you want to talk about him for?"

"Well… I have been talking about him with Elizabeth recently, and I was simply curious to know your own opinion of him," Teyla replied, her expression now becoming slightly inquiring in nature as she looked at him. "It is simply that… well, I have been attempting to understand the way you perceive him as opposed to the way that he is perceived by my people, so as to better improve the ties between us. Since you are not one of the military personnel- and hence not directly required to obey Colonel Sumner's orders regarding him-, I felt it would not be a conflict of interest to ask for your honest opinion of him, ignoring your need to consider Colonel Sumner's orders to capture him."

"Really?" Rodney said, his tone neutral as he looked reflectively around his lab for a moment, evidently taking time to collect his thoughts on the matter before he spoke once again. "Uh… just to make sure, Sumner's not going to hear about what I say here, right?"

"Not at all," Teyla assured her with a brief shake of her head. "Whatever you tell me will remain between us, I assure you."

"Glad to hear it," Rodney replied, shooting her a brief, grateful smile as he paused in thought for a moment before he spoke again. "Well… personally speaking- and I'm only even considering this because I actually _saw_ him when he drew away that energy thing; I wouldn't even be thinking this if I didn't know for a fact that he was out there-, when it comes to the Phantom, I'm really…"

He paused again for a brief moment, as though considering what he was about to say, before he spoke once again. "Well, I'm kind of ambivalent about the guy, when I think about it."

"Ambivalent?" Teyla repeated in confusion.

"Kinda feeling two different emotions about the same thing; it's complicated, I know, but that's just how I feel," Rodney said dismissively before he continued. "Anyway, my point is, while I'm more than a bit annoyed at the idea that we have somebody walking around here who knows more about Ancient technology than I do and _still_ isn't willing to talk with us about it- I mean, seriously, what's with the whole secrecy thing he's got going on?-, given that he's saved the city as a whole at least once since we came here- plus, of course, his little save of us last night; given how long he's apparently meant to have been hanging around here I think it's safe to say he'd have learned the control necessary to pull off a trick like that-, I'm more than a bit inclined to cut him a break."

"So… you believe that he means us no harm?" Teyla asked, wanting to ensure that she had understood her new teammate before she said anything else.

"Well, I think that he might _cause _some by not telling us about the technology in here that we might trip by accident, but I don't think he'd actually _do _anything that would cause us harm, if that's what you mean," Rodney replied, briefly turning back to his equipment before he realised that Teyla was still standing in the lab rather than having left after he'd given her his answer. "Is there something else?"

For a moment the young Athosian leader was silent, clearly uncertain about saying what she was about to say, before she finally nodded resolutely and looked up at the scientist once again.

"I… I have a theory about how the Wraith were able to find us on the planet yesterday," she said, the slightly anxious look on her face making it clear that she was at least slightly afraid of getting into trouble for what she was about to reveal but nevertheless determined to say it.

"You have?" Rodney asked, looking at her in confusion. "What is it?"

"It is… complicated," Teyla replied, before she reached underneath her hair behind her neck and removed a necklace, subsequently passing it to Rodney. "Can you… analyse this for me?"

"Huh?" Rodney said, as he took the necklace from her and looked at it in confusion. The actual string that formed the necklace he instantly dismissed as nothing remarkable- it looked like nothing more than the usual material that would be found in a civilisation on the same level as the Athosians- but the actual 'locket'- or whatever the correct term was- was actually rather interesting. It may have been only a simple metal circle with some kind of small green gem in the centre, but even the non-artistically-inclined Rodney couldn't help but admire the amount of craftsmanship that must have gone into this thing, given the Athosians' apparent lack of metallurgical tools based on what he'd heard from Sumner and Ford…

Shaking his head to force himself back on track- one of the curses of being a genius; sometimes when faced with trivial questions he tended to start thinking about wider 'issues' before he could stop himself-, Rodney turned back to look at Teyla.

"Uh… it's nice?" he said uncertainly, looking at the woman before him in confusion. "Just… what do you want me to _do_ with it, exactly?"

"Find out if it is emitting a… signal of some kind," Teyla replied, pronouncing the words uncertainly but nevertheless continuing to meet the scientist's gaze. "I have… reason to believe that you will find something."

"Really?" Rodney said, trying to conceal his natural scepticism as he studied the necklace he now held in his hand. For a moment he thought about simply rejecting the idea instantly- the concept of something like this being the reason for the Wraith's knowledge of their attacks was almost ridiculous-, but when he recalled some of the _other _things that the Stargate program had encountered over the years according to the files- the age-accelerating nanites, the ZPMs, the various time-manipulating devices such as the Asgard time dilation device-, the concept of a locket acting as a tracking device of some kind was hardly _that _ridiculous.

_Besides_, Rodney mused, as he reached over to turn on his laptop and connected it up to one of the scanners they'd brought in the event of them attempting to trace radio signals of some sort, placing the locket under it even as he began to run the scans, _it's not like it's going to take much time to confirm or deny this particular theory either way; just a few minutes on a broad-spectrum scan, and_…

His eyes widened.

"Huh," he said, staring in surprise as he read the information currently displayed on the laptop in front of him. "What do you know?"

"What _do_ I know?" Teyla repeated, looking at the scientist in confusion.

"This thing _is _giving off a signal…" McKay said, looking up at the Athosian woman in surprise. "It's not powerful enough to send a signal through subspace, but it is there; my guess is there are probably relay devices that probably pick up the transmission and alert the nearest hive ship on certain planets…"

"Such as the planet we returned to yesterday?" Teyla asked, looking inquiringly at Rodney. "It was the former location of one of their ships, after all; maybe they wish to keep those locations monitored to protect themselves from any attempts to attack them while they hibernate?"

Despite himself, Rodney had to admit that he was impressed; for a woman who'd been living in a hunter/gatherer society only a couple of months ago, Teyla was starting to grasp the essentials of scientific principles pretty well.

_Of course_, he mused, allowing himself a brief moment of satisfied thought, _with regular access to me during our mission training sessions, how could she _not _improve her scientific expertise from such a basic background-_

Mid-sentence, another thought occurred to him.

"What made you think the locket was the reason?" he asked, looking at her. "I mean, no offence, but the idea of this locket having a transmitter isn't exactly the kind of thing that I'd expect you to think of; what gave you the idea that it was behind the Wraith thing?"

"It was the Phantom," Teyla replied simply.

"Oh, right, that makes sense," Rodney said, shrugging casually as he reached over to continue his earlier experiment before his brain caught up with what he had just heard.

"Hold on; the _Phantom _gave you that idea?" he said, looking up from his equipment to stare at her in surprise. "When did he do that?"

"He…" Teyla began, pausing for a moment as she looked uncertainly around herself before continuing. "He visited me in my room last night and told me about it."

Rodney blinked.

_That _was unexpected.

"He actually _told _you that this locket was a transmitter?" he asked, picking up the object in question and holding it in front of Teyla.

"He said that he believed it was involved in how the Wraith managed to discover us during our last trip off-world; beyond that, he said that I should ask you to find the evidence for further confirmation," Teyla replied, as she turned to look earnestly at the scientist. "Please, you must _not _tell Colonel Sumner that the Phantom told us about this; there is no telling how he shall react to it if he knows that it comes from the Phantom."

"But it's _genuine_-" McKay began, only to stop as he thought more about what Teyla had said.

He had to admit, the Athosian had a point; Colonel Sumner probably meant well, but Rodney had been in the medical bay when he'd learned that it was apparently the Phantom that had been responsible for the gateship making it through the Stargate before the time had run out. Like when the Phantom had lured that energy creature through the Stargate, he'd acknowledged that the man's actions had helped them, but at the same time he'd made it clear that he objected to the man's independent manner of doing things; he could have simply told someone how to operate the chair in that manner rather than assaulting one of the expedition staff to do it himself.

If Sumner _knew_ that this information came from the Phantom, even if McKay had confirmed it before he knew what he was looking for, it might at the very least put the information on somewhat shaky ground with Atlantis's military commander…

After a moment's thought, McKay shrugged slightly as he looked back at Teyla.

"Well, I won't tell him where you got the idea from if you won't," he said finally.

Despite the serious implications of the discovery they had just made, Teyla couldn't help but smile slightly back at him.

They had discovered their first potential breakthrough in their new struggle against the Wraith.

All that they needed to do now was report it and figure out a way to exploit it for themselves.

* * *

As McKay and Teyla discussed the implications of their latest discovery, neither knew that the man responsible for them making it in the first place was currently sitting in one of the nearby maintenance shafts, a slight smile under his mask as he studied them.

Talking to Teyla and allowing her to tell McKay about him had been a risk, of course- it had taken all of his courage just to try giving Elizabeth that shield device, and he'd had prior experience to help him determine that she wouldn't hand him over to Sumner at a moment's notice- but he'd felt that it was a risk worth taking on the McKay front. He might have some ideas about Athosian culture- they were a surprisingly well-travelled group, for all their limited technology; he'd visited quite a few planets where they seemed to have spent at least some time during his travels, judging by the similar clothing and distinctive crops and herbs he'd seen in some markets while in a cloaked jumper scouting for Wraith and food- but Doctor McKay had been more of an unknown factor; the man was a genius, but he was also more than a bit of a pain when it came to scientific breakthroughs, given that he seemed to often try to almost take credit for other people's discoveries…

But, when you got down to it, he'd seen enough to know that McKay wasn't a bad person; he was just sometimes a bit too caught up in his own genius to realise that other people could have their own opinions on things.

Plus, of course, it was somehow… nice… to know that it wasn't only Elizabeth and the Athosians who thought that Sumner was being a bit over-the-top with his attitude towards him; the expedition leader's opinion might be the one that mattered most to him in the current situation, of course, but he hardly wanted to rely solely on her good will in the event that he was ever actually captured (He was good at staying hidden, but he wouldn't kid himself into thinking that he was so good he'd _never _be caught; these guys were _very _good at what they did).

Now, as he watched them walk out of the laboratory, McKay already calling Elizabeth to ask for her and Sumner to meet him in the conference room, all he needed to do was wait to see what they decided to do with the information that he'd provided for them, and bingo; as the old saying went, Robert was his mother's brother.

He doubted they'd get much from their subsequent… acquisition (He'd long stopped thinking of the Wraith as being people; their automatic need to kill did little to endear them to him)… of course, but it was still likely that they'd manage to get _something_, no matter how small it might be in the large-scale picture of things.

He'd learned long ago in his new life that, sometimes, you couldn't do anything to affect the big picture; you just had to do what you could on the small scale and hope that it would be enough to turn the tide in the long run.

* * *

"So," Elizabeth said as she sat in the conference room, a still-not-quite-one-hundred-percent Sumner sitting to her left as Teyla and Doctor McKay stood opposite her, studying the locket she held in her hand, "you're saying that _this _is the reason you were attacked?"

"Precisely," McKay confirmed, nodding at her as he briefly exchanged a glance with Teyla whose underlying motive Elizabeth couldn't immediately determine before turning back to her. "As far as I can determine, it can't transmit through subspace or anything like that, so our best guess is that the Wraith have relay devices on certain planets that pick up the transmission and subsequently send off a signal; given that the last planet we were on was used as a location for one of their main ships, it seems like that the Wraith

"If you had this when you were a child," Sumner asked, looking critically at the Athosian woman standing before him- his body still hadn't totally recovered its strength from being attacked by the giant insect, although Beckett assured him that he'd be back on his feet in a couple of days-, "then why weren't you attacked then?"

"Doctor McKay speculated that the locket was only activated when it was picked up by Captain Gemmel while I was showing him the ruins during your initial visit to Athos," Teyla replied. "I had possessed the locket as a child when it was given to me by my father, but I lost it among the ruins years ago."

"As you might recall, Gemmel had the Ancient gene; that's probably why he activated it when it had been dormant for centuries beforehand," McKay put in, a satisfied smile on his face as he looked over at the two expedition leaders. "As we've already established, at some point the Wraith and the Ancients were at war. Therefore, it only makes sense that, at some point, they would build a device capable of allowing them to track Ancients. The device probably shut down after it went for centuries without detecting any Ancients, only to be kicked back into action when Captain Gemmel picked it up; any Athosian wearing it would have been just another human, but Gemmel's gene evidently worked well enough for him to set it off instead."

"So, essentially, when the Wraith came after you on that planet, they came because they detected the signal from this?" Elizabeth asked, looking thoughtfully at the locket in her hands.

"So, if we can find any _other _planets with these relay devices on them…" Sumner mused, nodding thoughtfully as he looked at the device in Elizabeth's hands.

"We could maybe use it to set a trap for them," McKay confirmed, nodding at the military commander. "I've already started trying to figure out how to detect the presence of relay devices on other planets; if we can find a likely-looking location, we might just be able to spring our own little surprise on the Wraith… if that's all right with you, sir," he added, nodding respectfully over at Colonel Sumner.

"Permission granted," Sumner replied, a slight smile on his face as he nodded back at McKay. "Nice work, Doctor; we might just be able to turn the tide of this conflict after all."

* * *

The subsequent mission went off about as well as could be expected. Having examined the next few addresses available from the Ancient database for any signs of the relay devices that sent a signal from the locket to the Wraith, McKay finally found a decent location, on a planet where the Stargate was located amid a small collection of ruins and ships had difficulty landing, thus forcing the Wraith to come for them on foot if they were going to come at all.

Having lain various explosives around the ruins, arming themselves with stun-guns and flash grenades to better take the Wraith by surprise, the team for the current mission- consisting of Sumner's usual team and around half-a-dozen extra marines- had found themselves confronted by three Wraith foot soldiers and one Wraith leader, distinguished from his fellows by his lack of armour and long dark coat. The explosives had almost instantly eliminated two of the Wraith soldiers, the third one choosing to activate a self-destruct system implanted into his armour rather than be captured, but, thanks to Teyla's actions, they had managed to successfully capture the leader of the Wraith 'strike force', Teyla keeping him occupied with her stick fighting long enough for Sumner to take the Wraith by surprise with one of their own stunners.

* * *

With the assault team having been debriefed and the Wraith technology that had been acquired from the bodies taken off to some of the labs for study- with strict orders not to take apart the stunners until the scientists were certain of putting them back together-, the newly-captured Wraith was left to stand silently inside the cage where the Atlantis expedition had imprisoned him, staring around at his surroundings with evident contempt as two guards waited outside the door to the prison area; given the Wraiths' apparent telepathic abilities, nobody wanted to remain in a room with one for longer than was necessary.

The status of the city he now found himself in was almost pathetic, when the Wraith reflected on it; these people were clearly not the long-lost adversaries of the Wraith, the Altereans, but they used their technology and thought that it would grant them the power necessary to oppose the Wraith.

They had ruled this galaxy for the better part of the last ten thousand years; did these people, who clearly had not been in this city for even the merest fraction of that time, believe that they could succeed where the Altereans had failed?

They were Wraith.

They would prevail.

_Nothing _could stop them…

The faint sound of footsteps outside the 'cell' prompted the Wraith to look up in the direction of the sound, only for his eyes to narrow as he saw a dark figure, apparently wearing black, standing in one corner of the room, staring pointedly in his direction.

"Again?" he said, allowing himself a brief grin as he stared at the new arrival. "Your kind is persistent; I would have thought that you would have given up by now."

The figure simply stood silently in the corner, looking at the Wraith in a manner that was difficult even for the Wraith's superior night-vision to determine in the dim lighting that dominated the cell. After a moment's silence, the Wraith spoke again.

"You waste your time," he said briefly. "I will provide you with no information."

When the man standing before him- and he was increasingly sure it was a man; the figure's bearing gave no suggestion that it was female- continued to meet his statements with only silence, the Wraith spoke again.

"You might think that you've won a victory by my capture," he said, grinning slightly as he moved ever closer to the walls of the cage where the figure stood outside, "but by bringing me here, you've only hastened your own doom. It's only a matter of time before the others of my kind come to rescue me, and when they do…"

He allowed himself a brief pause in order to ensure that his adversary- he was one of his captors; that made him an adversary by definition- was still paying attention before he spoke once again. "There will be nowhere in this world you can hide."

For a moment, the silence continued to dominate the room, until the figure stepped out of the shadows and into the dim light surrounding the cell, the faint blue-green lighting instantly striking the silver mask the figure wore…

If it were possible for the Wraith to have heart attacks, the appearance of this figure would have caused one.

The Wraith hive ships rarely exchanged particularly detailed information with each other, mainly due to the low level of technology possessed by the various other civilisations that existed throughout the galaxy. The lack of any force in the Pegasus Galaxy that possessed enough power to stand against them meant that there was rarely any need for more than a few hive ships to know about any potentially significant threat to the Wraith's continued supremacy in this galaxy. The only rare exceptions to this rule included a few distant planets where it was believed some remnants of the Altereans' technology remained- a world where any Wraith darts attempting to cull the population were never found again, worlds where Wraith hive ships had taken such damage in the past that none had ever dared to return again-, and, of course, the man currently standing before the Wraith now.

In all of the Pegasus Galaxy, this man alone had done more damage to the Wraith in the past ten years than they had sustained in the previous thousand, using technology that they had hoped never to witness again.

The Wraith might be arrogant, but they knew that, in the end, they'd only survived the war with the Alterans thanks to sheer weight of numbers rather than any superior skill on their part. He'd initially dismissed these people as a threat due to their apparent lack of skill with the technology he now witnessed- they'd only used simple ballistic weapons when they had captured him- but if _this _man was working with them…

He would need to _significantly _re-evaluate their potential threat to Wraith dominance of this galaxy.

"_Phantom_…" the Wraith hissed, his eyes wide with fear as he stared at the figure before him, the man in question staring silently back at him with his arms folded under his long black cloak. "You are _here_…"

As the Phantom advanced towards the cage, the Wraith could not help but step backwards slightly; even the knowledge that the cage would not allow the Phantom inside from this direction any more than it would allow him to get out did little to help his comfort in this situation.

If he had been facing any other human, he would never have allowed himself to show this kind of weakness, but with all access to his hive temporarily cut off from him, and faced with the one man in all the galaxy to have gone up against no less than _three _Wraith Lords simultaneously and come out the victory, he doubted that there were many Wraith in his position who would not show fear.

"What do _you _want?" he hissed, trying to regain his original control over the situation; no matter how terrible the Phantom's reputation, he would _not _allow his fear to control him.

After a moment's silence, the Phantom spoke.

"Make sure you play nice," he said, a slight smirk visible at the left corner of his mouth, the right side partly concealed by the mask that had become his most distinguishing feature among all Wraith. "Also, if you get out…"

He left the sentence hanging in the air, but the Wraith understood the implication all too well.

Even if he managed to escape captivity here, the Phantom would be waiting for him.

"Remember that," the Phantom said simply after a few seconds' pause, evidently wanting to make sure that the Wraith understood what he was being told.

With that, the Phantom turned around and walked away from the cage, melting back into the shadows that filled the room before he vanished from the Wraith's sight.

* * *

AN: OK, since the next few eps aren't going to be SIGNIFICANTLY altered by the Phantom's presence- substitute Sumner for Sheppard and take away his ability to manipulate the hallucination generated for him by those mist-things and you've pretty much got everything you need to know about what happened so far-, next chapter jumps straight to one of my all-time-favourite _Atlantis _episodes, featuring the moment when the Phantom finally breaks his silence and speaks to the expedition…

Guess which ep I'm talking about?


	11. The Power of the Music of the Night

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: OK, just to clarify, this chapter takes place approximately three months after the last one, during which time the events of "Childhood's End", "Poisoning the Well", "Underground" and "Home" have all taken place, with this chapter beginning with a brief look back at how those episodes turned out here before the events of "The Storm" begin. Also, anything you don't see here happened pretty much the same way that it did in the original episode, with the obvious exception of Sumner replacing Sheppard

The Phantom of Atlantis

As she sat in her office, staring reflectively out at the gateroom below her, Elizabeth sighed slightly as she reflected back on the events that had taken place since the expedition's arrival.

All in all, in her opinion, while the situation hadn't been as bad as she might have expected- after all, they had come through so far with a fairly minimal amount of casualties and learned some potentially useful information about their new adversaries in this part of the galaxy-, it definitely could be going significantly better. Given their general lack of resources such as medical supplies, forming alliances with other civilisations wasn't proving as easy as it had been for Earth; they might have access to the technology of the Ancients, but they were still learning so much about it that they were reluctant to give anyone else access to it before they were certain they wouldn't give them something that could be harmful in the long term. Their recent experience with the Genii was evidence enough of that; the Genii might have achieved a technological level of culture approximately equal to Earth's abilities in the 1950s, but their lack of knowledge about the dangers of radiation had left most of their people in a potentially dangerous medical situation that Elizabeth doubted they could recover from on their own.

Admittedly, the fact that the Genii had attempted to steal a gateship and various quantities of C4 explosive from them simply because a mission to gather data from a Wraith hive-ship went wrong due to outside influences and found it easier to blame the expedition for the mistakes limited the amount of pity Elizabeth felt for them, but she still saw it as wrong that the entire race should suffer because of the mistakes of their leaders. If only the Genii had been willing to work with them rather than trying to take what they wanted, they could have acquired a valuable ally, but their determination to take control and their inability to accept that the expedition causing the Wraith to wake up early had only been an accident rather than a deliberate act of malice- coupled with the death of one of their men simply because he and Teyla had disagreed over what to do about one of the Wraith prisoners- had driven a wedge between their cultures that Elizabeth wasn't sure anything could effectively repair.

Still, as far as Atlantis's trading prospects went, things really weren't going as badly as they could have turned out, thanks in no small part to the efforts of the Athosians. After their recent discovery of a major continent only a few minutes' flight away by gateship, most of the Athosians had moved to the continent to start farming once again, with only a few such as Teyla and Halling, who had already accepted positions among Atlantis's offworld teams, remaining on Atlantis in order to continue working with their assigned offworld teams and help the expedition establish trading relations with some of their old allies before Athos had been culled. Despite their efforts, however, it would take at least another couple of months before the Athosians had anything like enough crops to provide something to trade with, to say nothing of being able to provide the expedition with sufficient food supplies for their own uses. In the meantime, the food packages they had received from M7G-677 after enhancing the force field that protected them from the Wraith had helped their food situation on at least a short-term basis, and Bates and Halling's subsequent efforts with the Manarians had also provided them with an at least partial supply of food while they waited for the Athosians' crops to grow (The rapid breakdown of relationships with the Genii had been somewhat disappointing, of course, but Elizabeth's previous attempts to negotiate with the Goa'uld- looking back on her days as the temporary commander of the SGC, she couldn't believe how naïve she'd been back then- had shown her that sometimes it was just impossible to make the other side see your point of view even if you could see theirs).

Elizabeth just wished that she could get over the more… _personal_ issue that had been bothering her for the last couple of weeks; ever since their encounter with the mist creatures when they'd thought that they'd found a way back to Earth without having to worry about the shield activating when they tried to dial from Atlantis, to be more precise.

During her recent 'visit' to Earth- it might have been an artificially-generated hallucination, but it was still as close to being real as she was ever likely to achieve given their continued inability to dial any address in the Milky Way without activating the shield over the Stargate-, when she'd been 'reunited' with Simon, even when she'd been told that Atlantis was going to be militarised in response to the threat posed by the Wraith, her thoughts had never been totally on the man she'd once planned to marry, or even the city that had become her home…

Even when the illusionary Simon had offered to finalise their relationship at last, Elizabeth had found herself unable to stop thinking about the Phantom.

Admittedly, after she'd 'learned' about the plans to militarise Atlantis in the hallucination, her thoughts had been mainly focused on if he would remain safe with that many soldiers available to hunt him down simply for apparently wanting to remain secret, but the fact remained that, even when she'd been with Simon, a part of her had always wondered how the Phantom was faring back on Atlantis, if Sumner's forces had caught him by now, if someone had discovered the shield device he'd given her where it remained hidden in her room…

She just couldn't understand her own train of thought on this specific issue at times; even when she had been reunited with Simon in the hallucination, _all _her thoughts had remained focused on the Phantom. She had tried to focus on being back with Simon, of course, but no matter how hard she'd tried to remind herself that she was back on Earth and the issue of the Phantom was no longer something she needed to worry about, she kept on starting to worry about him once again.

It was ridiculous; even if she'd been _on _Atlantis, it was unlikely that she would have actually been able to do anything to help the Phantom if he'd been captured without having Sumner or the military commanders accusing him of having influenced her actions somehow. Besides, he'd lasted this long without her taking any actual action to try and help him; what were the odds that he'd need help at this stage when he hadn't needed it beforehand…

There were so many reasons why she shouldn't have been worried about the Phantom when she 'got back' to Earth, and _none _of them had made her feel any better; she simply couldn't shake the concern she'd felt whenever she thought about him while she was in that hallucination. If only she had something _else _to occupy her attention…

"Doctor Weir?" a voice suddenly said from her door. Glancing up, Elizabeth was greeted with the rare sight of Peter Grodin looking almost afraid as he stood in her doorway, swallowing slightly as though trying to gather strength to tell her whatever he had discovered to leave him in that condition.

"Doctor Grodin?" she replied, standing up to look curiously at her assistant. "What's the problem?"

"We just received an urgent message from Sergeant Stackhouse when he was taking Teyla and Halling to the mainland for a visit," Grodin replied. "It would appear that we have a large- _extremely _large- storm heading right for Atlantis."

Elizabeth blinked.

She would have been the first to admit that she was nowhere near a science expert, but if Grodin was looking this anxious about a storm, she had a strong feeling that it wasn't going to be anything like a simple one.

"How large _is _'large'?" she asked, as she stood up to look at her assistant better.

"Large enough to cover apparently twenty per cent of the planet, hit the entire continent, and then move on directly to Atlantis," Grodin replied grimly.

Elizabeth swallowed.

She didn't need degrees in meteorology to know that something that big could _never _be good…

The question was, how bad would it turn out to be?

* * *

An hour later, with Stackhouse, Halling and Teyla having returned to the city, Elizabeth had called the three of them into the conference room, where they were discussing the implications of this latest discovery along with Colonel Sumner, Doctors McKay and Zelenka, and Lieutenant Ford.

"Is it actually possible for a storm to _get _that big?" Sumner asked McKay, looking slightly critically at the gateship 'crew' who'd discovered the problem; evidently, while Sumner might believe what the Athosians thought they had seen, he wanted to confirm whether it was possible in the first place. In the past Elizabeth might have considered such a concern excessive, but given what they'd already learned about the Wraith's apparent telepathic abilities she supposed that it only made sense to make sure that they weren't getting in a fuss over something that might not even technically be there; nothing could be taken for granted when facing an enemy who could influence what you were looking at.

"Actually, it is… well, theoretically, anyway," McKay replied, having taken a few moments before the meeting to go over the discovery with Zelenka and prepare a display that was now presented on the screen behind them; Elizabeth assumed that it showed weather graphs, but she would be unwilling to swear to it.

"You see," he continued, as he walked away from the screen to sit back down, "this planet is basically the same size as Earth. Now, hurricanes on Earth never get as big as this bad boy because once they hit the shore, the brakes get put on. Without as much landmass to slow it down here, it's just, uh, gaining momentum."

"_Both_ of them are," Zelenka added, raising one finger where his hands were clasped below his chin.

"Yes," McKay confirmed, nodding briefly at the Czech.

"_Both_ of them?" Elizabeth repeated, looking at Zelenka as she hoped she'd heard him wrong even as she knew she hadn't.

"We saw only one," Halling said, looking at McKay in confusion.

"It only _looked_ like one," McKay answered briefly, his attention still on his laptop as he continued to speak. "Now, according to the Ancient database, every twenty or thirty years the sea gets unseasonably warm. Now that, for reasons too boring to get into, means that hurricanes are much more likely to occur."

"Well," Zelenka began, pushing his glasses slightly up his nose as he spoke, "like El Nino, the ocean-"

"Like I said, too boring to go into," McKay interjected.

"_Focus_," Elizabeth said briefly; whatever else happened here, she was not going to allow the two men to start an argument in a situation like this.

"Well," McKay continued, as though neither she or Zelenka had never spoken, "basically, if you have a situation where there are a bunch of hurricanes out there, the likelihood of two colliding is greatly increased; that's what's happening."

"It's more like a merger than a collision," Zelenka clarified, hand gestures emphasising his points as he spoke. "They are intersecting and combining their power."

"_And_," McKay added, finally drawing the matter away from the meteorogical details of the problem and back to their more immediate issue, "it's headed right towards us."

After exchanging glances with the rest of the people in the room to ensure that they understood what they had just learned, Elizabeth decided to tackle the most obvious question first.

"You just said the Ancients experienced these storms every twenty to thirty years," she said, as she looked at the scientists. "Atlantis must have some sort of precautions put in place."

"Well, in the past, when they weren't submerged so far underwater that surface conditions weren't an issue, the Ancients tended to use the shield to protect them…" McKay said, before trailing off as he looked uncomfortably at the group of people around him

"By your tone, I take it there's a problem with using that option now?" Sumner replied.

"Yes; whenever the Ancients had to deal with these storms, they were using _three _ZedPMs at potentially full power to operate the shield," McKay replied, nodding at the commander. "We have _one _ZedPM with maybe twenty percent of its full power capacity- maybe even fifteen; I can't be entirely sure- and what data I've managed to gather from the database suggests that three ZedPMs working in tandem proportionately use less power than one at a time- there's all this stuff about them working together to reduce entropy, very scientific and we don't really have the time to go over it-, so-"

"Can you get to the part that explains why our only having one ZPM is a problem in this situation?" Sumner asked, looking critically at McKay. "I get that we'd be using less power than they'd have, but if three of them can keep this place going for ten thousand years-"

"During which, as far as we know, the city was totally uninhabited- except for maybe this 'Phantom' guy we've been hearing about, and even if there's any truth there the presence of one man would cause such a minimal drain on the power that it barely matters either way- and the shield was expected to do nothing but keep the water out; right now we're expecting it to provide power and comfort facilities for around a couple of hundred people _and_ endure some seriously powerful severe weather conditions," McKay countered. "We can get the shield _up_, no problem, but I really can't be sure if it'd last long enough to sustain the shield against the kind of torrential bombardment we'd be dealing with here."

"The city lasted for ten thousand years underwater-" Elizabeth began.

"As I already pointed out, the water was just _there_; it wasn't actually battering against the city at gale force speeds while maybe even hitting it with several thousand volts of lightning in the process," McKay countered as he looked over at her. "The high wind alone would cause some _serious _structural damage, and then there's the potential for tornadoes and electrical activity as a result of the thing passing over a landmass before it reaches us…"

He shook his head. "I'm not saying that the ZedPM won't be able to generate enough power to protect us; I'm just saying that I can't guarantee it can protect us for the whole storm."

"And, even if it did, it would be so drained that we'd lack the ability to raise the shield when the Wraith finally find us after using so much power to protect us from this threat," Sumner concluded, nodding grimly at the scientist. "So, with that in mind, do you have any way of guaranteeing that the shield will last for the duration of the storm?"

McKay simply looked blankly back at him.

"Not… _really_, no," he said, evidently trying not to look embarrassed at the admission. "The problem is that the people who built this city knew they had a forcefield capable of holding back anything Mother Nature or, for that matter, the Wraith could throw at them, and they had ready access to the power supply the city needed to _create _that forcefield. Without that protection, Atlantis is remarkably fragile."

"Even our conservative calculations project widespread structural damage if the city's exposed to the worst of the storm for more than a few minutes," Zelenka added.

"Flooding could sink the city entirely," McKay added- just to show that he still had more to add to the situation, a part of Elizabeth's mind thought.

"How could something as big as Atlantis just… _sink_?" Ford protested, looking incredulously at the scientists.

"Ask the _Titanic _construction team; it's possible," McKay replied briefly.

"_Titanic_?" Halling repeated, looking curiously at the scientist.

"Supposedly unsinkable ship back on Earth that hit an iceberg on its first voyage; not really relevant to the current problem except as an example," McKay replied briefly.

"So…" Sergeant Stackhouse said, looking uncomfortably between his assorted superiors, "you're saying that if Teyla, Halling and I hadn't discovered this, we-"

"We would be in even bigger trouble," Elizabeth said briefly; as much as she understood the man's train of thought- how often had she wondered if there wasn't something she could have done by this point to make Sumner think better of the Phantom (And why could she _not _get her thoughts away from him?)- this wasn't the time to start thinking about what they could have done differently to deal with this situation.

"All right," she continued, as she turned back to look at McKay and Zelenka, "what's the plan?"

"By my calculations," McKay began, glancing over at Zelenka as he spoke, "we have just under, what, twelve hours until the storm hits, so…" he trailed off slightly as he spoke, "uh… we plan to _have_ a plan…"

"Yeah," Zelenka confirmed.

"…by then," McKay concluded.

Elizabeth wondered briefly if it was possible to get away with being angry at someone for _not _being arrogant; couldn't McKay have made himself appear a _little _more confident than he was?

* * *

A couple of hours later, with the scientists still pouring over possible ideas in the briefing room and the rest of the expedition preparing to evacuate the Athosians from the mainland and packing their bags to move to Manaria for the night, none of them were aware of the black-clad figure crouched in the maintenance tunnel above Elizabeth Weir's office, watching the expedition members through a small hole he'd created in the wall years ago as they rushed desperately to salvage what personal belongings and equipment they could before the storm forced them out of the city.

He supposed that this situation was at least partly his own fault- if he'd stored his entire ZPM supply here the expedition wouldn't even have this problem- but after he'd first realised the potential destructive power of the ZPMs he'd thought it inadvisable to keep too many of them in the city. If the Wraith had ever managed to infiltrate the base, all it would have taken was one of their number to find his ZPM stockpile and the Pegasus Galaxy's ultimate nightmares would have practically unrestricted access to a near-unlimited power supply, and that was if the Wraith who'd discovered them in that theoretical scenario had been _smart_.

If they'd been stupid, on the other hand…

All it would have taken was one bad shot from a Wraith who had no idea what he was looking at, and he'd have been left with, at the very least, some significant damage to Atlantis, and at most the entire planet and a significant portion of the solar system would have been destroyed. He'd run a few computer simulations to work out what might happen in the event of a worst-case-scenario- in this case a full-scale Wraith invasion- a long time ago, and while none of the results had been encouraging, the ones where he kept the ZPMs on Atlantis rather than on the abandoned moon where he'd hidden them invariably turned out to be the worse ones.

While he might want to ensure the Wraith never managed to gain access to Earth, he was equally reluctant to put himself in a position where he would have been forced to destroy Atlantis. Given the gene-sensitive equipment, the Wraith were incapable of using most of its technology, and with the shield protection system he'd erected all those years ago it was equally impossible for them to ever gain access to Earth, so destroying Atlantis would accomplish nothing but deprive the universe of the Altereans' crowning glory…

Whatever his reasoning, the facts remained; the expedition was currently facing a potentially serious threat from the storm that was currently bearing down towards them, and at the rate things were going the only way Atlantis was going to _definitely _survive (McKay might be a pain in the neck but he had his facts right; there was no way to know for sure if the current ZPM would have enough power to keep the shield up for the duration of the storm) was if he provided them with the location of his ZPM 'stash'.

He wasn't happy about it, but it wasn't like he had many alternatives available to him; the city _couldn't _be allowed to fall, and given the Manarians' connections to the Genii he was extremely reluctant to leave the expedition dependent on them for more than a place to rest for the night (Just the thought of them doing _that_ much made him uncomfortable, but he consoled himself by reminding himself the Genii would hardly be daring enough to attack almost the entire expeditionary force- to say nothing of the Athosians- just to try and get some explosives; any kind of attack on a group that large would inevitably cause heavy casualties for the Genii, and whatever else those people were, they weren't suicidal).

Maybe if he left Elizabeth another note with the 'gate coordinates for the moon where he'd left the ZPMs, she might be able to-

The sound of hurried footsteps hurrying through the control room broke off that train of thought, prompting him to turn around and look in the direction of the control room as Doctors McKay and Zelenka hurried towards Elizabeth, where she was currently studying a laptop with a couple of the technicians (That was something he really liked about her; she was willing to stay in touch with all levels of the expedition staff). Reaching up to his ear, he activated the radio he'd taken from the supply storage all those months ago and tuned it in to Elizabeth's frequency; he wouldn't normally listen in on her conversations, but if McKay and Zelenka had a plan to save Atlantis he wanted tohear it before he made any rash decisions.

"_What is the_ one _thing keeping us from having a shield_?" McKay said, almost sounding as though he was continuing an old conversation rather than beginning an entirely new one.

"_That would be-_" Elizabeth began as she turned to look at the two scientists.

"_Sufficient power_," McKay replied simply, cutting Elizabeth off before she could finish (The observer always hated it when people did that; why ask a question if you were just going to answer it yourself?). "_And what does the mega-storm from hell have lots of_?"

"_Power_," Elizabeth replied again, her tone slightly uncertain but still evidently fairly sure that she knew where this conversation was going.

"_In the form of…_?" McKay asked, waving a hand promptingly.

"_You want to build a windmill_?" Elizabeth said, her tone evidently questioning the sanity of the people before her as she stared at the scientists (Not that the man in the shaft could blame her; the idea of them whipping up a windmill to try and power the shield was _ridiculous_, even if they'd had enough time to get everything together…).

"_Electricity_," McKay corrected after a moment's pause; for a moment his implied _Are you dim_?, even if nothing personal had been meant by it- it was just McKay being McKay- was enough to make the man watching the conversation from above want to hit him.

"_Atlantis is designed to withstand substantial lightning strikes_," Zelenka explained. "_There are lightning rods all over the city_."

"_All those rods are channelled into four main grounding stations_," McKay continued.

"_In turn, those grounding stations discharge electricity back into the ocean, keeping Atlantis safe from massive electric shocks due to lightning strikes_," Zelenka added; really, for two people who argued as much as these two they could be almost unnervingly in sync with each other when they had some major discovery or theory to explain.

"_Now_," McKay said, picking up the explanation once again as though he'd never even stopped talking, "_many of the hallways are lined with a superconductive material that allows a safe, low-voltage transfer of power throughout the city_-"

"_Which, of course, means_-" Zelenka began.

"_Yes, I'm getting there, I'm getting there_," McKay said dismissively, cutting Zelenka off mid-sentence before he refocused his attention on Elizabeth, excitement evident in his voice at the possibilities of what he was currently discussing. "_Let's say the grounding stations _weren't _around. Every time lightning struck the city, those halls would become supercharged_."

As soon as their silent observer had heard that sentence, he wondered whether he should classify McKay as a genius or an idiot for thinking of something that crazy.

It _could _work, of course, but the odds against them managing to channel and gather that much natural power in the time available were almost ridiculously against them…

"_So, wait_," Elizabeth began, apparently- he couldn't quite make out the expression on her face from where he was currently located- looking at the two men as though she was wondering what drugs they'd taken (Not that he could blame her; the plan sounded absolutely demented from where he was crouching), "_you want_-"

"_If we were able to _dis_able the grounding stations_-" McKay continued, apparently unconcerned about Elizabeth's reaction.

"W_hich we think we can_," Zelenka added.

"-_every time lightning struck the city, Atlantis would experience a momentary__ massive_ _power surge_," McKay concluded.

"_Now_," Zelenka continued, "_that energy, if it's channelled correctly_-"

"_Yes, of_ _course_ _if channelled correctly_," McKay said briefly before continuing, "–_could conceivably be used to charge up the shield generator _instead _of the ZedPM. Now, the more severe the storm, the more energy's produced, and the longer we can keep the shield running without forcing us to resort to the ZedPM_."

"_It's an ingenious plan, really_," Zelenka said, turning to McKay as the two of them seemed to relax more now that the

"_I'm inclined to agree_," McKay added, nodding in agreement at the Czech scientist.

"The only downside is we have no way of storing all that energy after the storm's over, and really, why worry about that right now?" Zelenka said casually.

"True; even if the Wraith _did _send any ships this way, we'd have plenty of warning to prepare and see about finding a new ZedPM…" McKay mused.

"Gentlemen," Elizabeth said, drawing their attention back to her. "_The city would survive_ without _use of the ZPM_?"

"Mmm…" McKay mused, his tone casual as he folded his arms and looked briefly upwards in a reflective manner, "_it might give us a better than ninety percent_-"

"Seventy," Zelenka corrected.

"Eighty percent chance," McKay concluded.

"_OK, so we should still evacuate_," Elizabeth said,t he statement partly a question as she looked at the two men.

"_Yes, but not just because of Zelemka's pessimism_," McKay interjected.

"Zelenka," the Czech corrected- really, why couldn't McKay get the guy's name right; it wasn't _that _hard- before he continued. "_If the plan works, the city will become highly charged with electricity. Really, the only safe place to be once the lightning begins to strike is in the Control Room_."

"Mmm," McKay nodded. "_We need to evacuate everyone offworld until the storm passes and execute the plan with the smallest team possible_.

"_OK, good_," Elizabeth said, nodding at the two men. "_Get on it_."

"_Right_," McKay replied, just before the listener terminated the connection; he'd heard everything that he needed to hear.

As far as plans went, McKay and Zelenka's idea seemed to have everything covered; the city's sole remaining ZPM could be kept in storage until the time came when they had no viable alternative available, the shield could be successfully maintained for the duration of the worst part of the storm, and the expedition members themselves could remain safe on Manaria until the time had passed.

In other words, he was almost certain that something was going to go wrong that none of the expedition could have predicted. The Manarians might not hand the expedition members themselves over to the Genii- as he'd reflected earlier, there were simply too many people, both expedition members and Athosians, for them to be captured without the Genii sustaining such serious losses as to make the mission's success, assuming it happened, a pyrrhic victory at best- but with Atlantis left with only a few people to defend it in the event of an attack…

It might just be paranoia; after all, the Atlantis expedition could offer the Manarians far more in the way of weapons and protection than the Genii ever could, even if they weren't willing to share everything with them at the moment…

On the other hand, as the old saying went, "Even paranoids have enemies"; just because it benefited the Manarians more to side with the expedition in the long term didn't mean they wouldn't think more about the short-term benefits of siding with the Genii instead.

That was the problem with forming alliances, really; most people in the Pegasus Galaxy were more focused on their own personal survival rather than the survival of anyone else. If they'd only see what idiots they were being by not thinking of anything more than their own skins, if they collaborated with each other on a more long-term basis than just the occasional trade for food they might have actually been able to make a dent in the Wraith's hold on this galaxy before now…

Well, the situation was what it was, and complaining about it wouldn't change anything; all he could do was keep an eye on the situation and be ready to get the vital equipment somewhere safe if he found himself in a worst-case-scenario situation.

He'd promised her a long time ago that he'd keep the expedition safe, and he was _going _to keep that promise even if Colonel Sumner continued to try and hunt him down afterwards.


	12. Darkness Stirs

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

With the last of the expedition members- with the exception of the gateship containing Lieutenant Ford and Doctor Beckett; the last small group of Athosian hunters were apparently taking their time getting back- having left for Manaria, and the two remaining marines left on guard in the control room in the event of any attempted uninvited guests, Elizabeth soon found herself in Doctor McKay's laboratory, standing opposite Colonel Sumner around a table in the laboratory as McKay went over the information on his laptop one last time.

"Right then," he said, his fingers rapidly flying over the keyboard as he spoke, "one last time for the non-scientists here; there are dozens, possibly hundreds of lightning rods placed strategically around the city. Now, normally all the energy these things capture is routed into four main grounding stations. In turn the stations ground all that energy into the ocean below."

"So," Sumner said, looking over at McKay, "once we disable those grounding stations…"

"We use the energy to power the shield," McKay confirmed, smiling slightly at the general.

"The city can handle that?" Elizabeth asked, looking uncertainly at McKay.

"Yes!" McKay replied, his voice displaying his eagerness at what they were about to accomplish.

"…Theoretically," he added, spoiling the effect in Elizabeth's eyes.

"When you say 'theoretically'…" Sumner said, looking questioningly at McKay.

"I mean theoretically; you _are _aware we're on a time limit at the moment?" McKay asked, looking pointedly at the colonel before he continued. "Anyway, Elizabeth, you take grounding station two; I'll take grounding station one, and Colonel, you take stations three and four."

"Which are _where_?" Sumner asked, his folded arms demonstrating his dislike for McKay's attitude; in all fairness, Elizabeth herself acknowledged that the Canadian scientist's habit of sometimes assuming you knew everything he did about a situation could be frustrating, but at least he always got the job done in the end.

"Oh, here and here," McKay replied, indicating the points in question on a screen displaying the city that was up on a nearby wall.

"And we are currently…?" the colonel continued, his gaze still fixed on the astrophysicist before him.

"Here," McKay replied, indicating an area in approximately the middle of the city. "I need to get done quickly so I can start working on the subroutines, and Elizabeth was complaining about her knee the other day-"

"Would any of these generators be near transporters?" Sumner asked, cutting off the scientist before he could continue (Elizabeth was already fairly sure that McKay had given Sumner the hardest part of the job for more personal reasons, particularly given that she'd never complained about her knees in her life; the two men might work together well enough on the team, but personality-wise they clashed surprisingly often about relatively trivial matters).

"Uh… yes, Elizabeth's is," McKay replied, looking at Sumner in a slightly sheepish manner, although Elizabeth couldn't tell if it was genuine or not.

"And mine?" Sumner asked pointedly.

"Uh… it's a brisk walk away," McKay replied.

"And by 'brisk' you mean 'far'."

"And by 'walk' I mean 'run'," McKay admitted, before continuing his explanation as though nothing had happened. "You'll need to radio in once you've got to your first station."

Sighing slightly, Sumner shrugged and stood back from the table.

"All right, let's do this," he said, looking over at the other two. "I'll see you later."

With that, he turned around and walked out of the lab, leaving Elizabeth and McKay to look at each other in shared frustration.

As a military commander, Sumner's record was excellent.

As far as his ability to form personal bonds with those under his command went, however, he definitely had a lot to learn.

"Well… best get to work," McKay said, shrugging slightly as he turned back to study the display before them. "Now, Elizabeth, the nearest teleporter to your grounding station is here…"

* * *

As the figure watched and listened to the two men standing on guard in the gateroom from his usual spot in the upper tunnel leading to the jumper bay- really, when there weren't that many people in the room sound could carry surprisingly well even without his use of the radio to listen in in case of a last-minute change of plan-, he couldn't help a slight smile crossing his face as he took in their conversation.

It was inane, it was pointless, it served no purpose in the current situation…

And that's why he liked it, really; he rarely got the chance to listen to any kind of conversation that _didn't _involve plans against the Wraith or something like that these days. The opportunity to kick back as discuss something as inane as what the expedition members missed from home was something he hadn't had the chance to enjoy that much, and he was grateful for the opportunity to do so now even if he couldn't contribute himself.

"_Bacon_," one of the men said in response to the other's question.

"_The one thing you wish you brought with you is bacon_?" the other guard said.

"_Hey, it's the food that makes other food worth eating_," the first man replied (Not that their unknown observer could disagree with his opinion; he'd always enjoyed a decent bacon sandwich himself back in the days, and he'd yet to encounter any meat the Pegasus Galaxy had to offer that was anything _like _as good…).

"_You wish you brought bacon to another galaxy_?" the second guard said

"_Yeah_," the first one replied. "_You asked me_-"

Before he could continue, the Stargate began to activate, the first three chevrons rapidly illuminating even as the two guards and their unknown observer turned to look at the sight.

"_Offworld activation_," the guard said, the original topic of discussion instantly forgotten as the two of them hurried over to the control panel.

"_Doctor Weir said no one should be coming back until tomorrow_," the other guard said, the confusion evident as his colleague activated the laptop positioned beside the DHD.

"_There's been an attack on Manara_," a woman's voice- one that the figure watching the scene below didn't recognise- said over the now-activated radio link. "_We've got wounded incoming. Lower the shield_."

The first guard took a brief glance at the console. "_They're broadcasting an Athosian IDC_."

"_Please__, before it's too late_!" the woman's said on the other end of the communication.

The man watching the scene from above them was rapidly beginning to dislike the situation he now found himself; what were the odds of the _Wraith_ attacking Manara just when the Atlantis expedition were present?

But, on the other hand, it wasn't _entirely _impossible to assume that

"_We are lowering the shield_," the first guard said into the radio before him

"_Whoa_," his colleague said, reaching out to grab his arm before it could reach the switch to deactivate the shield, "_let's get the OK from Doctor Weir_-"

"_They're under attack_," the guard countered, his tone clearly allowing for no argument in the current situation. "_Lower the shield_."

After a moment's hesitation, the other soldier reached over to punch in the code to lower the shield, the Stargate subsequently 'opening' to the world on the other side of the wormhole even as the guard who'd voiced the initial objection activated his radio.

"_Doctor Weir_," he said, as he and his colleague got to their feet and began to hurry towards the lower level to greet the new arrivals, "_there's been some sort of an attack on Manara. We have an Athosian party incoming with wounded_."

"_We're on our way_," Elizabeth replied briefly, before her radio connection terminated as well, drawing the man's attention back to the cloaked figures currently coming through the Stargate carrying a couple of stretchers.

They definitely _looked _Athosian, he couldn't deny that, but something about them didn't seem right… the woman currently speaking to the guards just didn't strike him as someone he'd seen before…

Then a tall figure dressed in a familiar uniform of dark green with brown edges swung off one of the stretchers, got to his feet, pulled out two pistols, and shot the guards before him with as little regard as a Wraith would show for its latest victims.

As the rest of the new arrivals shrugged off their cloaks, revealing identical uniforms and similar weapons- a lot less sleek and significantly bulkier than the expedition's weapons from Earth, but nevertheless a step up from some of the technology he'd encountered during his travels throughout the Pegasus Galaxy-, the true identity of the new arrivals became clear to their unknown observer; only a few civilisations had reached the level of technological development necessary to make weapons like that, and only one of those groups had a reason to come after Atlantis.

_Great_… the man above groaned, slumping against the walls of the tunnel as he took in what had just happened. _We've got a small Genii army inside the city, only one military and two civilian members of the expedition left to even _try _and defend it from them, and a massive storm bearing down on all of us; to say the situation is discouraging is a _serious _understatement_.

Even as the Genii began to spread out- their exact words eluded him due to their lack of a radio he could tap into, but all he needed to hear was "Cover the entrances!" to know that they were planning to settle in for a prolonged period-, his mind raced over his possible options in the current situation. He could jump down there and try to take out the Genii while they were still contained in the gateroom, of course, but right now he only had a couple of handguns on him against approximately two dozen trained Genii soldiers- he hadn't had time to take a more accurate count yet- and they were already too spread-out for him to see them all clearly enough from his current position. All it would take was for one of them to get in a lucky shot- he wasn't going to count on his presence being enough to shock them into submission; if these guys were gutsy enough to invade Atlantis they clearly didn't put much faith in the tales he'd tried to encourage to stop people looking for him- and he'd be dead, or at least wounded enough to make his continued attempts to help impractical at best.

However, while direct attack wasn't an option, a more subtle approach might at least put him in a better bargaining position to… encourage them… to leave the city without too much fuss. Given that this was the Genii he was dealing with, based on Sumner's report of their encounter, their most likely reason for being here was the acquisition of explosives with which to perfect their own nuclear weapons technology, thus allowing them to strike back at the Wraith (He briefly contemplated telling the Genii that there were too many hive ships for that to work but swiftly decided against it; even if they did believe he was real, their commander struck him as the kind of person who totally ignored anything that didn't fit his view of the world, which in this case almost certainly included the idea that the Genii alone deserved to live and defeat the Wraith).

With that in mind, his best bet to get them out of the way would be to move the C4 to a secure location- fortunately, his long time in the city had acquainted him with several locations that would probably fit the bill-, and then try and force them to surrender the hostages and leave the city in exchange for at least _some _of the explosives (Giving the expedition's entire supply of C4 to these guys would definitely be giving the child in the tinder-box the lit match; if they actually thought that the radiation was harmless to them with the kind of shielding McKay had described in his report, they'd probably blow up quite a few _innocent _planets before they realised how much they were screwing up with their experiments, but with a limit amount they might at least be more inclined to limit their tests).

_Plus, of course_, he mused, another couple of thoughts occurring to him as he took one last glance at the Genii forces gathered in the gateroom, _I'll need to make sure that the Zero Point Module doesn't fall into their hands; even if they can't use it as a power source for anything, the last thing we need is them trying to use _it _as a bargaining chip of their own…_

_Oh, and there's still that other puddle jumper left on the mainland; might as well get off a message while I can_…

* * *

As she and McKay walked hurriedly towards the control room, their own individual grounding stations and the first of Sumner's already deactivated, Elizabeth had already activated her radio to inform Sumner of the latest turn of events; even if it turned out to be nothing significant, she had a duty to make sure that her military commander was kept up-to-date on the situation.

"Apparently there's wounded incoming," she said as she walked.

"_You're saying that we have people who were injured in a Wraith attack_?" Sumner's voice said over the radio, his tone clearly reflecting his scepticism.

"Yes, I acknowledge that it's odd-" McKay began.

"'_Odd' is not the word, Doctor; this goes against everything we have learned to date about the Wraith's M.O._," Sumner replied. "_Given what we know of the Wraith, if they'd attacked Manaria I wouldn't have expected much in the way of wounded; if they knew we were there the entire population of Atlantis and the Athosians would have either been culled or-_"

The sound of guns cocking in Elizabeth's face drove her attention away from her conversation with her military commander and to the more immediate issue of the group of unfamiliar soldiers standing over the fallen bodies of two of her staff, in strange uniforms consisting of dark greenish-grey and brown lining, pointing some primitive but nevertheless dangerous-looking guns directly at her and McKay.

If Elizabeth had been the type of person to do so, she would have sworn.

As it was, as two of the soldiers before them walked forward to grab her and McKay by the arms and force them into the centre of the gateroom, all she could do was hope that this latest turn of events would be explained sooner rather than later.

"Doctor Elizabeth Weir," a voice said from off to Elizabeth's right. Glancing up the stairs in the direction of the speaker, Elizabeth watched as a tall man with a weather-beaten face and an (In her opinion) ridiculously prominent nose stepped forward, looking at her with an annoyingly smug expression on his face.

"Yes," Elizabeth replied simply; if she'd learned anything from the hostage negotiations she'd conducted in her time in the U.N., it was that it was important to avoid antagonising the hostage-takers- and she and McKay were hostages; she wasn't going to assume otherwise- until you had a better idea of what they wanted.

"And you must be Doctor McKay," the man continued, looking over at the Canadian scientist. For a moment, McKay simply looked silently back at the man who seemed increasingly likely to be the leader of the soldiers, but then one of his people- a young woman with shoulder-length light red hair- stepped forward to stand beside him.

"That is him," she said, glaring coldly at the astrophysicist.

Before Elizabeth could ask the man who he was, he had suddenly reached out to take the radio she wore over her ear away, slipping it slightly uncertainly over his own as he spoke into it. "Would this be Colonel Sumner?"

For a moment, even as Elizabeth cursed herself for continuing to talk to Sumner as she approached the gateroom- this man must have overheard the colonel talking over the radio; he'd never have suspected that somebody else was inside the city otherwise-, there was nothing but silence on the other end of the radio connection, until the man spoke again.

"Do not attempt to deceive me; my men and I heard you talking to Doctor Weir when she entered the room containing the Stargate," he coldly said into the radio; whether he was bluffing or being honest Elizabeth couldn't be sure, and wasn't sure what she could do about it in the first place. "If you do not reply immediately, I will be forced to take… action."

Elizabeth might not know what this man meant by that comment, but, at the same time, she knew that she definitely did _not _want to find out what he was planning. After another brief silence,

"_This is Colonel Marshall Sumner_," the military commander said on the other end of the radio. "_What do you want_?"

"Simply return to the Gateroom via the shortest possible route," the commander said. "My men and I will be waiting for you."

With that he terminated the call and casually handed the radio back to Elizabeth, who took

"You seem to know a lot about us," she said, staring coolly at the man before her. "Who are you?"

"They're Genii," McKay said off to her left, his voice clearly showing his disgust at the soldier's actions (Not that Elizabeth could blame him; they'd been willing enough to help the Genii before they'd tried to steal the gateship and the Wraith data recorder).

"There's only one thing you need to know, Doctor Weir," the man before her said, his tone as self-satisfied as it had been when he first spoke. "As of right now, we are in control of Atlantis."

* * *

As she sat anxiously in the gateship with Lieutenant Ford, Doctor Beckett, and the last group of hunters, Teyla couldn't help but wish that she was already back on Atlantis, if not having already travelled through the Stargate to Manaria to be with her people. She was confident that they would be safe, of course- the Manarians were a good people, if somewhat reluctant to give something without any guarantees of receiving something in return- but that still didn't prevent her from feeling concerned…

Before that train of thought could progress any further, however, something came up on the viewing window at the front of the gateship, prompting Teyla, Ford and Beckett to look at the new display in surprise. Teyla swiftly abandoned her own attempts to read it- she recognised the written language as that used by her new friends, but she was still working on learning more than the essential basics of it; her training for becoming a member of Colonel Sumner's team had been more focused on military tactics and use of weapons rather than languages and writing-, but evidently Ford and Beckett understood what it said all too well.

"What the _Hell_…?" Lieutenant Ford muttered, as he glanced over at Beckett. "Am I reading this wrong, or is this thing in _English_?"

"Not just English, son… a totally coherent message…" DoctorBeckett replied, his eyes rapidly scanning the information before him even as they reflected his confusion at this latest turn of events. "'Genii in Atlantis… Weir, Sumner and McKay captive… get back here ASAP… P.'."

After a moment's pause, during which the three sitting in the gateship's control room processed what Doctor Beckett had just read, Lieutenant Ford voiced what they were doubtless all thinking.

"'P.'?" he said, looking over at Teyla. "You think this came from that 'Phantom' of yours?"

"He is hardly 'my' Phantom, Lieutenant; he has been the guardian of almost the entirety of this Galaxy for the better part of the last ten to fifteen years," Teyla countered, looking pointedly at her teammate as she spoke; she understood Colonel Sumner's reasons for disliking the Phantom's presence, but she still felt that the military commander would do well to show the man more respect than he had done so up until to this point. "In any case, it would appear to be the only logical explanation; according to this letter, Colonel Sumner, Doctor Weir and Doctor McKay have all been captured, and I cannot think of any soldiers in the last group whose names begin with 'P'."

"Look, whoever it's from, I think it's safe to say we can trust it; these 'Genii' buggers- they're the ones who wanted us to help them build nuclear weapons, right?- wouldn't have anything to gain by letting us know they're there," Doctor Beckett pointed out, before he sighed slightly as he stared at the message once again. "Too bad we can't actually _do _anything about it right now…"

"What?" Lieutenant Ford said, looking incredulously over at the doctor. "What are you talking about; we _have _to do something-"

"Take a look _outside_, hot shot," Doctor Beckett said, indicating the storm still raging around them with a wave of his hand at the main viewscreen. "We're not flying through this."

"Sumner, McKay and Weir were taken hostage, Doc!" Lieutenant Ford protested. "I'm not just gonna sit here while some guy who won't even let us know if he's really there-!"

"Neither one of us are real pilots," Doctor Beckett countered, pointedly ignoring the younger man's comments about the Phantom as he looked at his colleague. "It was a bad idea an hour ago; it's an _idiotic_ one now."

"We're gonna have to take our chances-" Lieutenant Ford began.

"Doctor Beckett is right, Lieutenant," Teyla cut in, her own anxiety about this latest turn of events concealed as she looked at her friend. "You are of no use to the hostages if you are dead; we must remain here until the weather improves and we can safely depart."

She had thought about saying that he was no use to the _Phantom_ dead, but Teyla knew well enough that such a line of argument wouldn't work; Lieutenant Ford was a good person, but he was in many ways Colonel Sumner's man, and had already made it clear more than once that he agreed with Sumner's view of the Phantom as a potential danger to the expedition.

She trusted that the Phantom- and this message _was _from the Phantom; Teyla was convinced of that much at least- could handle himself until they could make their way back to the city; she simply knew that mentioning such a fact to Lieutenant Ford would do little to help him the way he currently felt about the situation, given his commanding officer's own stance on the Phantom.

All that she and the rest of the people in the gateship could do now was wait and trust that the Phantom would do what he could for the hostages that remained in the city in the hands of the Genii…

* * *

AN: To anyone who thinks I'm making Ford a bit too 'military' as opposed to his more relaxed, somewhat jocular attitude in the show -, given that he could be VERY 'military-minded' when the situation called for it- such as when giving the rest of the team that briefing about the weapons they'd be using to capture 'Steve' in "Suspicions"- I'm assuming that part of the reason for that attitude was that Sheppard was the kind of military commander who was comfortable with informality, and didn't insist on people maintaining a 'professional' attitude unless the situation called for it, while Sumner is less relaxed about his duty even when he's not dealing with the latest crisis. Ford's still fundamentally the same person, it's just that in this timeline he's been more encouraged to be 'professional' rather than to be 'casual' even when he's off-duty in Atlantis


	13. A Message from the Ghost

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

As Elizabeth stood in the control room, McKay just behind her and Genii soldiers all around her, she was unable to stop an at least slight feeling of distaste as the commander of the Genii forces walked past them, staring at the technology around him in the same manner that she had seen on the faces of the rest of the expedition when they had arrived; eager to see and learn all that they could about this new location, while at the same time trying to remain professional.

It could be considered arrogant on her part, Elizabeth knew, but it just seemed… _wrong_… for somebody outside the expedition to be looking at the city in that manner without being invited. The expedition would have freely shared their technology with the Genii if they had been willing to form an alliance, but instead this man and his fellows had felt the need to take by force what they could have acquired in an alliance. The expedition members might not be as advanced as the Ancients themselves, but their civilisation had still spent the last seven years learning about some of the discoveries that the race had made and the history that had motivated them; just because they didn't know everything about Atlantis didn't meant that they didn't know enough to safely live in the city.

Plus, there was the fact that the Genii were still learning about nuclear power; at least when Earth had begun to learn about the Ancients' genetic evolution and some of their other scientific advances they'd already gathered the basic scientific principles behind most of the technology. Even if they couldn't duplicate the Ancients' feats themselves, they at least knew enough to understand the possible consequences if they got into something without knowing what they were dealing with. Given the Genii's relatively low level of technology they'd almost certainly end up starting something they didn't know how to stop because they hadn't advanced far enough to stop…

The sound of footsteps coming from another corridor distracted Elizabeth from her train of thought, prompting her to look in the direction of the sound as Colonel Sumner walked into the room, hands up and gun in the hand, clutching the barrel to make it clear that he wasn't going to try and shoot the Genii.

"Colonel Sumner, I assume?" the commander said, looking at the Colonel with an almost mocking small smile on his face. "Lay down your weapon and come up here- and be assured, my men _will _shoot if you attempt anything."

Even as Sumner glared at the man before him, Elizabeth was relieved to see him obey the directive despite the evident distaste on his face; like her, Sumner was acknowledging the value of waiting for a better moment rather than trying to attack the Genii head-on in their current situation. As one of the Genii soldiers collected his P-90- emptied of ammunition, Elizabeth noted; at least that limited the possibility they'd have to deal with someone using it against them if they tried to fight back-, Sumner's hands were bound behind his back before he was marched up to the control room to stand beside her and McKay.

"Who are you?" Elizabeth asked, turning to look pointedly at the apparent leader of the Genii forces as her own military commander took his position beside her.

"Commander Acastus Kolya of the Genii," the man replied, as he continued to look around the control room. "This Atlantis is extraordinary– more than I ever imagined."

"What have you done with the rest of our people?" Sumner asked, glaring pointedly at the Genii commander as he turned to face the man in question.

"I'm quite sure they have no idea we're even here," Kolya replied, not even bothering to look back at Sumner as he walked past them to study one of the computer monitors.

"Then they're safe?" Elizabeth asked.

"Yes," Kolya replied briefly, continuing to study the screen before him- currently showing what appeared to be the weather patterns that had caused the storm, Elizabeth noted; she wondered if he even knew what he was looking at- without looking at her.

"How were you able to bypass the shield?" Sumner asked, looking at the Genii commander with only the slightest trace of anxiety on his face; as always, any potential security problem was his top priority.

"With a time-tested combination of strong drink and a weak mind," Kolya replied, still studying the screen before him; Elizabeth didn't need to be a diplomat to recognise Kolya's obvious attempt to demonstrate his control over the situation by declining to even bother looking at them.

"There was a time when our two peoples considered becoming allies," she said, walking forward slightly; if Kolya wanted to maintain control, Elizabeth was going to make sure he didn't have it easy doing so. "Why are you doing this?"

"You're in possession of supplies we vitally need," Kolya replied, finally turning around with a frustratingly neutral expression on his face; it was as though he felt that it went without saying that the Genii would need the supplies in question more than the Atlantis expedition. "Hand them over without difficulty and we'll leave peacefully."

"Or else what?" Sumner asked, stepping forward slightly to stand beside Elizabeth and look more pointedly at the Genii commander; even with his hands bound, the Colonel could still create a very imposing figure if he had to do so.

"We're both intelligent people, Colonel Sumner," Kolya replied, a smug little smile visible in the right corner of his mouth as he walked forwards once again. "I'm sure there's no need for me to demonstrate once again the… strength of my resolve."

"Which supplies did you have in mind?" Sumner replied after a moment's pause; judging by his still-resolute stance, Elizabeth had little doubt that he was simply asking the question to better establish the situation they were facing at present rather than out of any kind of inclination to give Kolya what he wanted.

"All of your stores of the C4 explosive, all of your medical supplies, the Wraith data device you stole from my people, and one of your ships," Kolya replied simply.

Elizabeth didn't even trust herself to speak; the casual manner with which Kolya practically demanded them to hand over half their possessions made some of the Goa'uld she'd met back at the SGC look humble by comparison. He didn't even seem to consider or care that they might need them as well; as far as he was concerned, if the Genii needed something, nothing else mattered so long as they got what they wanted.

"Is that _all_?" McKay asked, the sarcasm evident in his tone; evidently he had less of an inclination to restrain himself in the current situation.

"Look," Elizabeth cut in, stepping forward slightly in an attempt to make the Genii leader understand what she had to tell him, "what you're asking for is not easy. We've had to divert a lot of power in order to prepare for the storm. The armoury's safety doors have shut, which means we can't-"

"Just so we're clear," Kolya said simply, holding up a hand to stop her mid-sentence, "I know a lie."

"Your request just isn't reasonable," Sumner countered, stepping forward slightly to stand in front of Elizabeth as he addressed his Genii opposite. "Your culture's still learning about the full dangers involved in radioactive explosives; you can't possibly have developed enough to require our _entire_ supply of C4, and as for medical resources-"

"You're in no position to tell me what is reasonable and what is not," Kolya interjected, glaring back at Sumner; Elizabeth wasn't sure if the interruption was because Kolya didn't like being argued with or he didn't like the implication that the Genii weren't important enough to merit all the things he'd just asked for.

"How do we know that you won't kill us once we give you what you need?" Elizabeth said grimly, daring the man before her to try and give her any kind of reassurance that he would leave them alive.

"You don't," Kolya replied simply.

The simplicity of that statement reaffirmed Elizabeth's opinion of the man; evidently, as far as he was concerned, they should simply feel 'honoured' to have the opportunity to help the Genii, even if they ended up dead after 'doing their part'.

"Please show my men where they can find what they are looking for," the Genii continued, evidently unaware about her recent thoughts about him. "Colonel Sumner, you will remain with these men; be assured that, should you attempt anything, they will have no hesitation about shooting you."

As the young woman- judging by McKay and Sumner's reaction to her, Elizabeth was guessing that she was the 'Sora' that had been mentioned in the Genii mission reports- stepped forward to grab Elizabeth's left arm and hustle her away with a couple of soldiers, another group of Genii taking Sumner down towards the gateroom to better keep an eye on him, Elizabeth sent up a brief prayer to whoever was listening that Kolya wouldn't do anything permanently damaging to Rodney; the last thing she needed was for the expedition's chief scientist to be crippled because an arrogant git couldn't take 'No' for an answer.

The subsequent walk between the gateroom and the storage rooms was more of a haze in her mind than anything else; Elizabeth had spent most of her time trying to come up with a plan that would allow her, Sumner and McKay to get out of their current predicament without risking loss of life or losing the city, only to come up with nothing that she could use. She retained enough awareness of her surroundings to point out when they came up to the medical storage room- as much as she hated having to hand over the entirety of their medical supplies, if she at least pretended to go along with the Genii's demands at the moment there was still a chance of getting out of this situation-, but it was only when she finally reached the storage room where the Wraith data device had been kept that she turned her attention back to the immediate group of soldiers that remained with her. By this point there were only two- a dark-haired man with a beard and maybe a couple of inches in height over her and the woman Elizabeth was increasingly convinced was Sora-, but Elizabeth knew her limitations well enough to know that even these two were too much for her to handle, given her lack of professional training.

"The device is just over there," she said, indicating a table off to one side as she opened the door. "Just give me a moment, and I'll get it out."

Seemingly barely even registering her comment, the woman and the bearded man entered the lab behind her, the man moving over to study some of the computer displays while Elizabeth moved over to the table where the case containing the Wraith data device was stored, moving it onto the table just as the woman approached her.

"Where is Teyla Emmagan?" the woman said after a moment's silence, during which Elizabeth's gaze alternated between her and the case that was now before her.

"You know Teyla?" Elizabeth asked, looking inquiringly at the woman for any clue that her original assumption about her identity was correct.

"Is she here?" the woman interjected, her face displaying a cold, ruthless expression that did little to reassure Elizabeth. "In the city?"

"No, she isn't," Elizabeth replied.

As the woman looked away with a slightly disappointed expression, Elizabeth knew that she'd been right.

"You must be Sora," she said, trying to sound sympathetic despite her current situation. "I read the Genii mission report; I'm sorry about your father."

"He'll be avenged," Sora replied simply; the implication that her need for revenge went without saying left Elizabeth even more uncomfortable.

"Teyla didn't kill him," she countered, feeling the need to at least try and defend her friend in Teyla's own absence; after the woman had answered so many of her own questions about the Phantom, to say nothing of the aid she had provided Colonel Sumner as a member of his team, Elizabeth hated the idea of simply allowing Sora to blame Teyla for something she had no control over.

"No," Sora replied in an almost sarcastic manner, as though she felt that Elizabeth was insulting her intelligence. "She left him to die."

"She had no choice-" Elizabeth began.

"Are you finished?" Sora interrupted angrily, glaring coldly at her.

For a moment, Elizabeth allowed herself to look regretfully at the younger woman- was it possible that she was simply trying to deal with her grief over her father's death by transferring the blame for the action to Teyla rather than admit her own feelings of failure to herself?-, but shook it off and turned her attention back to the case before her. As much as she wanted to help, she was a diplomat, not a psychologist; even if Sora had been willing to ask for help, it was doubtful that she could have provided much.

Besides, from what she'd seen of Kolya so far, Sora's response had left her starting to wonder if arrogance was part of the Genii's nature almost as much as it had been part of the Goa'uld's infamous genetic memory; they seemed almost incapable of accepting any evidence that suggested that they weren't the most important people in the Pegasus Galaxy, and, by extension, that any views other than theirs were the right ones.

"All of the information we downloaded from the Wraith ship is still on this device," she said as she removed the Wraith data device from its case, subsequently handing it to Sora and the bearded soldier.

* * *

As Elizabeth and the soldiers she had escorted earlier arrived back in the control room, she noted with only slight surprise that Colonel Sumner was still being kept under guard down in the main part of the gateroom near the Stargate; evidently they had been made aware of the storm that was currently approaching them and saw little sense in dividing up their forces unless they had to do so.

It was only when she entered the control room and saw McKay standing in one corner with his hand clutched over his right arm around the elbow, blood staining his fingers and sleeve, that she broke her stride, hurrying over to stand beside the Canadian scientist while the Genii soldiers walked towards Commander Kolya.

"Ah, you're here," McKay said, smiling and wincing practically simultaneously as she examined his arm, barely registering the Genii soldiers coming from the direction of the armoury with a distinct absence of weapons; right now her more immediate concern was making sure that one of her few remaining allies was in good shape.

"What did they do to you?" she asked, wishing that Sumner was over here rather than down in the main gateroom; he might not have been a doctor, but surely as a soldier he'd have to know _something _about battlefield medicine in case he was injured during a mission.

"I tried to keep my mouth shut, I tried, I just- I couldn't" McKay said in a rapid tone of voice, clearly almost desperate to say his piece, before trailing off as he looked at something behind her. Turning around, Elizabeth was only partly surprised to see Kolya standing there, holding a radio in his right hand as he looked critically at them.

"What is the meaning of this?" he asked.

"I honestly have no idea," Elizabeth replied honestly; what Kolya was doing with a radio when he'd been after the C4 was a complete mystery to her.

"It's a radio," McKay said, as Kolya turned his attention back to the radio; Elizabeth could almost have sworn that he was enjoying the opportunity to tell Kolya what to do. "The arrow points to the 'talk' button."

Staring at the Canadian scientist in an impossible-to-read manner- Elizabeth could only hope that McKay hadn't made things worse for himself by talking back like that, Kolya raised the radio to his mouth and pressed the button.

"This is Commander Kolya of the Genii," he said simply.

"_I wish that I could say it is a pleasure to speak to you, Commander, but that would be a lie_," an unknown voice said from over the radio; a quick glance at McKay was all that Elizabeth needed to do to confirm that he didn't recognise the speaker either. "_You might appreciate knowing that the C4- and, as an added bonus, the Zero Point Module- have been transferred to a safe location that you will be unable to discover no matter how much time you have available to you, meaning that, right now, you have nothing but your hostages to bargain with… and I can assure you, if you want what you came here for, you _should _be prepared to bargain if you want to get out of this city in one piece_."

If the situation had been less serious, Elizabeth would have laughed at the suddenly shocked expression on McKay's face when the voice revealed that he had moved the ZPM. As it was, however, the implications of his concern- had the presence of the ZPM played a more central role in his calculations for the power necessary to generate the shield than he had let on at the time?- did little to comfort her in their current plight.

"_If you agree to allow the hostages to gate offworld unharmed_," the voice continued,"_I will grant you access to the C4 supplies and you may depart with what you sought; if not… well, I am sure you have learned about the storm currently bearing down on us_."

"Indeed," Kolya replied, a slight smirk as he spoke. "Just as I am also aware that, while this 'Zero Point Module' of which you speak is responsible for the city's power supply, it is not entirely necessary for the plan that Doctor McKay has concocted to save the city-"

"_And, let me guess, you wish me to deactivate the final grounding station and then depart, leaving the technology of the Ancestors in the hands of the Genii while the expedition members are left to fend for themselves_?" the voice interjected, sounding almost bored as its owner spoke to the commander. "_A tempting offer in its way, but I must decline; even if morality did not prevent me from abandoning the expedition like that, I have too great a claim to this city to abandon it to the likes of you_."

"You and your people have arrived in this galaxy barely months ago, and you dare to believe that you have a greater right to this city than we who have lived here our entire lives?" Kolya retorted, a sneer on his face. "Your arrogance is-"

"_I am not one of the expedition, Commander_," the voice interjected. "_I was here long before them, and have allowed them to remain_-"

"You have '_allowed_' them to remain?" Kolya interrupted, his tone clearly demonstrating his disbelief of the words that he had just heard. "Who are you that you believe you have the right to decide who 'should' remain here?"

"_Come now, Commander_," the voice said over the radio, the speaker sounding almost amused as he spoke, "_you cannot honestly have expected to mount an assault on my city and _not_ encounter me; even without the knowledge of my encounter with your people during that attempted culling a few years back, I have, after all, gone to not insignificant lengths to ensure that my name and the pertinent details of my history are known throughout this galaxy in my campaign_."

"What do you mean?" Kolya asked, looking critically at the three expedition leaders before him as though asking them for answers, despite the fact that Elizabeth, for one, knew that she had none to give. "Who are you?"

"_I am the Phantom of the Ancestors, Commander Kolya_," the voice stated, its tone low as it addressed the Genii commander. "_And believe me, if those hostages are harmed, you will make me _very _unhappy_."

For a moment, silence dominated the control room, all of those listening to the radio conversation apparently stunned into silence- Elizabeth knew that she was, at least; the Phantom was actually speaking in _their _defence?-, before Kolya spoke again.

"Your claim to be the Phantom is obviously false," he said, the now-familiar arrogance once again evident in his voice. "If you were the true Phantom, you would side with _us_ over these invaders-"

"_I have allowed the Atlantis Expedition from Earth to remain in this city only because I know that they will use its technology for the benefit of those who cannot defend themselves in this galaxy_," the voice countered, the speaker's tone now shorter than it had been earlier; evidently he resented Kolya's attempts to disprove his claims. "_Your people, on the other hand, attempted to force me to remain with you after I had done nothing but act in your defence when the Wraith came to your world; I merely sought to inquire if you required any further aid, and you attempted to imprison me unless I gave you exclusive access to my technology_."

"The Genii are the most advanced race in this galaxy-" Kolya began.

"_Technologically speaking, your abilities _are _impressive, yes, but _morally_ your goals leave a significant amount to be desired_," the Phantom replied; Elizabeth could almost have sworn there was a slightly teasing tone to his voice as he spoke at that moment, even as his solemn tone made it clear that he still considered their actions repugnant. "_You are willing to sacrifice other civilisations if it means that you survive, you attempt to steal from those who have what you require even if they are willing to share some of it with you, and you betray and lie to those who should be your allies against the Wraith. I will make this simple, Commander; either you permit the Atlantis expedition to remain and depart with only _some _of the C4, or I will guarantee the destruction of this city, regardless of whether or not I am still within it. I shall meet you at the last active grounding station to discuss terms; Doctor McKay shall inform you where it is. Come there, alone and unarmed, and we can attempt to decide on terms for an arrangement that will be mutually satisfactory; is that acceptable to you_?"

After a moment's silence, Kolya nodded.

"Very well," he said simply. "I shall see you there."

With that he terminated the radio connection and looked over at two of the soldiers. "Go to the grounding station and eliminate the man you find there."

The soldier he had just spoken to hesitated.

"But sir…" he said, looking awkwardly at the Genii commander, "if it _is _the Phantom-"

"It is _not _the Phantom; it is merely a member of this expedition attempting to intimidate us into surrender," Kolya countered, glaring resolutely at the man. "Now go to the grounding station and eliminate whoever you find there, or I shall take you outside the city and lock the doors."

The soldier nodded and departed, followed by one of his colleagues, leaving Elizabeth and McKay to simply look anxiously at each other.

Elizabeth might not have been certain what McKay's view on the Phantom was, but she also knew that, right now, he may well be their only hope to get out of this situation alive while also retaining control of Atlantis; if nothing else, the speaker- assuming it _was _the Phantom; she didn't recognise the voice, but it wasn't like she'd memorised the voices of every single member of the expedition- made it clear that he preferred having them remain in control of the city rather than the Genii.

The only question was, would whatever he was planning prove to be enough to turn the tide in their favour? She doubted that he actually intended to surrender the city, of course- what he'd said to the Genii commander made it clear that he disliked their actions and attitudes towards the rest of the Pegasus Galaxy as much as she did-, but she still had no idea what he was planning to do instead…

* * *

As he stood between the fourth grounding station and the door that connected it to the rest of Atlantis, his long cloak blowing in the wind and his favoured stun-blaster weapon in his right hand, he studied the Life Signs Detector he'd picked up from the jumper when he'd sent the message to the remaining would-be evacuees back on the mainland- unfortunate acronym, of course, but it got the job done and he'd never been able to come up with anything snappier himself-, and noted with only slight disappointment that there were apparently _two _people near him rather than the one he'd been expecting.

_So much for the diplomatic solution_… he mused to himself, looking reflectively at the grounding station controls now before him; he knew how to turn them off, of course, but until he'd managed to get Kolya to talk to him he was reluctant to give up his only viable bargaining chip, so for the moment the station would remain on until he'd determined what these two new arrivals were going to do.

For a moment he contemplated trying to get Kolya to call off this crazy attack by telling him that the odds of any Genii possessing the Ancient gene were so slim as to be non-existent- in all of his travels throughout this galaxy he'd only encountered a few worlds where the inhabitants had the ability to use Ancient technology, and on those occasions there had been specific evidence that Ancients had remained on that world to have some kind of influence on their culture-, but he swiftly decided against it. Given what he'd seen of Kolya's attitude, the man would probably just assume that he was lying and say something about how _he _was the arrogant one to assume that the expedition were closer relatives to the Ancients than the Genii people were; right now, since this attempt at diplomacy clearly wasn't going to work out, he'd just have to take these guys out now and go back to his original plan of using the threat of leaving the grounding station active to force Kolya to listen to his terms.

After waiting for a moment or two to see if they took any action only to be met with nothing- evidently they were waiting for him to activate the grounding station before they actually started trying to stop him-, he crept around to the other side of the grounding station in an attempt to see his current opponents, subsequently moving towards the door when he'd determined that he couldn't see them from that angle to press himself up against one edge. For a moment he waited, his eyes fixed on the screen in his hands, but when one of the dots before him began to move he quickly spun around the corner, firing a red blast at the man that sent him to the ground in a heap with a decent-sized smoking hole in his chest. As the other Genii soldier hurried forward, he turned and ran towards the nearby railing, hoping to get a better shot at the other man while providing himself with a decent shield, only for any hope of that idea working out being dashed when the Genii opened fire and struck the control console for the grounding station.

_SHIT_! he swore inwardly as he dived over the railing before him, spinning around mid-jump to fire a quick blast at his opponent- a tricky skill to learn given his cape, of course, but something he'd picked up thanks to the practice he'd put in after he started wearing the thing-, sending him to join his colleague. Quickly picking himself up, he ran back towards the grounding station, but only required a cursory glance to confirm what he already knew; the bullets that his would-be killer had just fired had wrecked the panel beyond his own ability to repair it.

Growling low in his throat, he walked over to the nearest dead Genii, yanked the radio communicator off the man's wrist- he still had the radio he'd used earlier, of course, but what he had to say would be more effective coming from a Genii radio-, and raised it to his mouth.

"Allow me to explain _where _you messed up, _Commander _Kolya!" he yelled into the radio over the roaring wind, internally torn between anger at the damage Kolya had done and glee at what it did to the Genii's chances to take the city; call him self-centred, but if Elizabeth and her people couldn't have the city, he was going to make certain that the Genii couldn't. "Firstly, you lost two of your men in a pointless attempt to take me down. Secondly, those _idiots_ damaged the control panel before I could deactivate the grounding station, which means that you may well have _doomed _this entire city. Thirdly, _you have just lost all of what little credibility you had with me_!"

After a moment's silence- during which he thought he heard McKay's voice over the line; evidently the man was just as angry at what had just happened as he was-, Kolya spoke once again.

"_You killed two of my men_," the Genii commander said simply.

He couldn't believe it; the city was facing imminent destruction because the Genii soldiers had suffered from a serious case of itchy trigger fingers and destroyed the one piece of equipment they needed to even have a _hope _of coming through this- particularly since he had no inclination to let these guys have access to the ZPM, even if it meant Atlantis was destroyed in the storm-, and all that this… _idiot _could focus on was _two men_ that had been killed in self-defence?

"You already killed two of the expedition; consider this conflict even and leave!" he roared over the weather.

"_I don't_ _like__ even_," Kolya replied.

"I am not finished yet!" he said, wishing that Kolya was there right now so that he could punch the bastard in the face.

"_Neither am I_," Kolya replied coldly. "_Say goodbye to Doctor Weir, blasphemer_."

His blood ran cold, and it _wasn't _from the 'blasphemer' comment (He'd encountered more than one world where people actually _prayed _to him for protection- he generally tried to stay away from those ones as they just made him uncomfortable- and he was certain that Kolya wasn't one of them; the guy was just trying to remind his soldiers that they 'couldn't' be facing the 'real' Phantom); the commander had just managed to precisely target what he would freely admit was his main weakness without even trying.

"The city has a self-destruct button!" he yelled, hoping desperately that this would be enough; he _couldn't _let Elizabeth die…

"You hurt her, I'll activate it!" he continued; he knew that he was beginning to sound desperate, but then Elizabeth Weir had made him do a lot of things he wouldn't have done for anyone else since the expedition had first arrived. "And then _nobody _will get Atlantis!"

"_Even if it exists_," Kolya replied coldly, "_you need at least two senior personnel to activate it… and I'm about to take one of them out of the equation_."

With that, the radio fell silent, leaving him staring desperately at the small device in his hands.

"Kolya?!" he yelled into the speaker, pressing the button as he tried desperately to attract the commander's attention. "Kolya?!"

When his pleas were still met with nothing but silence, he gritted his teeth and tried another tactic; as much as he hated to do this, it was the only thing that might even remotely tempt Kolya not to go through with his last threat.

"You can have a ship!" he said, the desperation in his voice hopefully drowned out by the volume he had to reach to be heard over the wind that now surrounded him. "I'll fly it out of here for you myself!"

After silence met his plea once again, whatever remained of his rational side finally snapped.

"_KOLYA_!" he screamed desperately into the radio. "DON'T DO THIS!"

He knew that losing control right now was the worst thing he could have done, but with the life of the most remarkable woman he'd ever met at stake right now, rational thought was pretty much out the window.

Even as the rain began to pour down on him, making his cloak heavy with water and leaving faint drips around his mask's eyeholes, he continued to stand in silence, praying that the Genii commander wouldn't do what he'd just threatened to do, even as the silence made it increasingly likely that his newest enemy had carried out his threat.

He couldn't let this happen… he couldn't lose her… he'd only just got her back after almost two decades of waiting… he _couldn't _lose her…

"_How is this for credibility_?" Kolya's voice suddenly cut in over the radio, breaking his train of thought; he wasn't even sure how long he'd been standing there waiting for an answer. "_Doctor Weir is dead_."

For a moment he was silent, his mind almost unable to process the three simple words he had just heard.

_Elizabeth was dead…_

The woman who had come to mean so much to him in such a short space of time, the only woman he would have truly lived for in a galaxy that had so far given him nothing but things to die for, the woman who had given his entire existence meaning where it had once had nothing, both when he had first arrived in the city and when _she _had first arrived…

She was dead.

He had failed her.

After he had waited so long for the chance to see her again, she had been taken from him before he had the chance to truly reveal how much she meant to him…

Behind his mask, his eyes narrowed as he clenched his empty hand, rage burning behind the silver metal that had so long covered his face he could barely even recall what had once been underneath it.

_Fine_.

If the Pegasus Galaxy wanted him to be the Phantom he had become rather than the man he might have been, he would _give _them the Phantom.

All that might have inspired him to try and be human once again had just been taken from him anyway…

"Congratulations, Commander," he said coldly, raising the radio to his lips once again. "You have just accomplished something that only the Wraith have done before now."

"_Which is_?" Kolya retorted arrogantly.

"You have earned my wrath," he stated simply. "Tell your followers to pray to the Wraith, because the Ancestors will not be able to save them now; thanks to your actions, the Genii have just forsaken all rights to the protection of the Phantom."

With that said, he terminated the radio connection, turned around, and ran back into the city, one of his guns already drawn as he studied his Life Signs Detector for any trace of the Genii.

Commander Kolya had killed Doctor Elizabeth Weir.

It was time to 'thank' the commander for giving him a reason to let out the beast within.

Even if it meant tearing this city apart, not a single Genii would leave this planet alive…

And he would take _particular _care to make Kolya's death a slow one.

* * *

AN: Just to assure you all before I start receiving death threats, Elizabeth _is _still alive, just as she was in the show; Kolya is, as ever, just being a bastard and trying to hurt his enemy. Oh, and for anyone wondering, yes, the gun the Phantom uses here against the Genii soldiers _is _the same type of weapon as Ronon's gun, but he is _not _Ronon Dex; his true name will be at least partly revealed in the next chapter or two


	14. Power Over You Grows Fainter Yet

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: OK, just to clarify, any scenes that don't appear here- like the scenes with Teyla, Beckett and Ford in the 'gateship' or McKay, Elizabeth and Kolya at the grounding stations, happen essentially the same as they did in the show with only minor variations in dialogue; the only significant difference is that Sumner and two other soldiers were brought along with Kolya's 'group' when the grounding station was repaired, as Kolya wanted to keep an eye on the colonel himself to ensure he didn't try anything in the control room and needed extra guards to keep an eye on a trained soldier like Sumner (He was confident enough that he'd be able to handle Elizabeth and McKay himself if he tried anything in the show, hence why he didn't bother with back-up there)

The Phantom of Atlantis

As the Phantom charged grimly deeper into the heart of his city, his gun raised as he stared resolutely at his LSD- he _really _didn't like that acronym- for any signs of the Genii, he forced his mind to block out the pain that felt like it was trying to tear his heart out of his chest.

He'd promised himself long ago that he would protect this city to repay Doctor Elizabeth Weir for what she had done for him so long ago; he might have failed to save _her_, but he'd let himself become food for a Wraith Queen before he let the Genii gain access to the city that she had come so far to save.

Glancing at the Life Signs Detector in his hand- he might not be able to come up with anything else to call it, but at least the full name didn't have the implications of the acronym-, he smiled resolutely as he saw a small group of 'dots' running towards his current location (He was grateful that he'd taken the precaution long ago of encoding the city's internal sensors not to register his own life signs; it might have seemed like paranoia at the time, but at least this way it ensured that he couldn't be tracked by anyone who might have attempted to take over the city and use it against him). They might know _approximately _where he was based on the idea of him travelling from the grounding station towards the control room, but he was the only one who would actually know where _they _were; that gave him a significant advantage.

Glancing at his weapon once again, he quickly shifted it to 'kill' mode- he wanted to make this quick and simple; he'd take out two of the men coming his way and then question the third before dealing with him- and then continued to hurry down the corridors towards his destination; there was a decent-sized room a few metres down the corridor from his current location- he was fairly sure that it was the location of one of the storage tanks for the city's water filtration supply, but he wouldn't like to swear to it; his knowledge of Ancient tech tended to be limited to what would help him in a fight, with his theories about what the rest of the stuff here did being only theories- that would make the _perfect _place for an ambush.

* * *

As he led his small strike force through the corridors of the city of the Ancestors, Larim forced himself to ignore the nagging voice in the back of his head that told him that their current actions would result in nothing more than bad luck for the Genii people. For all the doubts that he might possess about Commander Kolya shooting the two soldiers when they had arrived in the base, the fact remained that he had been correct when he denounced the blasphemous pretender to the Phantom's title as what he was; it was _not _the Phantom they faced, but merely a member of this expedition attempting to intimidate the Genii into surrender.

For that crime alone, this man deserved to suffer; the Phantom's name was _not _a tool that could be used to frighten the Genii into surrender like they were mere children, and he would _never _side with those who denied the Genii their rightful control of this city.

As he and his men advanced further into the city that would soon serve as the stronghold from which the Genii would wage a new war against the Wraith, Larim constantly kept his ears alert for any sign that the figure was near to them. Laden had done what he could to direct them to the route that the impostor was likely to take if he truly sought to deprive the Genii of the city, but at the same time it was solely based on guesswork due to the apparent inability of the sensors to detect his presence.

As he led the other two soldiers in his small group through the door to another room, he allowed himself a brief moment of anxiety as he took in the smoke before him- had something been damaged in this part of the city?-, but then he saw a small canister in the middle of the room and realised that the smoke was nothing than a distraction-

His brain froze as the implications of that word hit him.

_A distraction_…

In which case, there was something inside this currently-darkened room- whether it was this dark due to the storm or due to the Phantom impostor having apparently disconnected the city's main power supply, Larim didn't know- for them to be distracted _from_…

Before he could communicate this revelation to his colleagues, there was a strange crackling sound that sounded like a combination of a musical note and an electric shock, sending both of his men falling to the ground as a tall figure in a long dark cloak fell from the ceiling, swinging around to glare in his direction with an ease that would have made even the most well-trained of Genii soldiers envious.

Even with the darkened room making it hard to see clearly, Larim knew who he was now facing; the silver mask that covered the figure's face was instantly recognisable even in the dim lights of the city around them. Pictures of the man before him had been circulated amongst the Genii ever since he had saved them from a culling only a few short years ago, only to leave them after they had asked for his assistance in defending them from the Wraith on a more permanent basis.

Larim's blood ran cold.

It _was _the Phantom…

"Good evening," the man- the _Phantom_- said, his expression grim as he glared at the only Genii still standing in the room before him. "I will make this simple. Tell me what I want to know, and your death will be quick; attempt to refuse, and I will just have to torture you until you _do _tell me."

Larim blinked in shock.

Had the _Phantom _just threatened to _kill_ a human?

"But… but you _cannot _do that!" he protested, staring in shock at the man before him. "You are-"

A brutal punch to Larim's face left him lying on the floor, blinking in pain and shock at the sudden coppery taste of blood in his mouth. Looking up as he clutched at his now-aching jaw, Larim was unable to repress a slight shiver as he saw the Phantom clearly glaring at him under the mask that had become a symbol of hope for the humans of this galaxy and had so suddenly become a symbol of fear for him.

"Do _not _seek to tell me what I am; your commander already attempted to define my actions according to what _he _feels I should do, and he has evidently ignored my efforts to make him see that he is incorrect if he feels the need to send you and your associates after me," the Phantom countered, before he raised his weapon- a strange one, the design of which Larim had never seen before- and aimed it at him. "As I have already told you, you have a choice between making this quick or making this unpleasant; tell me where Kolya is, and it will be quick, I promise you."

"B-but… you are the _Phantom_!" Larim protested. "You are meant to _protect_-"

His sentence was cut off by a loud scream as the Phantom raised his weapon and fired it at Larim's left arm; Larim barely had time to register the sudden strange sense of pressure on the limb before his entire arm below the elbow vanished, the wound seemingly instantly cauterised by whatever had caused the injury even as it left the pain from the attack

"You and your people have forsaken any right to my protection by your cowardly actions against those whom I have granted the right to remain in this city," the masked man said coldly as he glared at Larim, his tone making it clear that he would tolerate no further attempts to contradict him. "I will ask you one more time, and then, if you still refuse it shall be your leg; _where_. _Is_. _Kolya_?"

"H-he… he has taken… the hostages to… to repair the… the grounding station!" Larim gasped; the pain in his arm making it briefly hard for him to focus on what he was saying, but the prospect of further damage to his leg gave him a compelling reason to continue.

"Which leaves how many people in the control room specifically and in Atlantis overall?" his captor asked, slightly squeezing the damaged wrist as he glared at his prisoner.

"Eight; Com… Commander Kolya took two others… with him to… to keep an eye… on the prisoners…" Larim said, desperate to halt any further injuries; if he was honest with the Phantom about the division of their resources- and he had little doubt that the Phantom could determine when he was lying- he might at least have some rest in his last moments. Even though he knew he was unlikely to survive this confrontation- the Phantom's tone made it clear that he would show the Genii no mercy for their actions here today, a prospect that terrified Larim more than he would admit even to himself-, no sense of loyalty to his commander could drive him to lie to the spirit of the Ancestors themselves, particularly with the amount of pain he was now in.

"Thank you," the Phantom said simply, before raising his gun and pointing it at Larim's face. "I would ask you to apologise to Eliza- _Doctor Weir_ for me, but after what you've done…"

He swallowed slightly, as though trying to control himself- evidently what he was discussing was something that had a profound emotional effect on him-, before he spoke once again. "After what you and your people have done today, you're not going anywhere _near _where she's gone."

* * *

As the Genii fell to the ground with a sizable portion of his head now missing, the man who had so recently been interrogating him turned around and began to run towards the control room, trying not to think too much about the bloody mess he'd just left behind him.

If the thought of doing what he had just done had crossed his mind merely an hour ago, he would have been disgusted at it; even when fighting the Wraith, he had always tried to make their deaths quick, perceiving it as a matter of necessity for the survival of the Pegasus Galaxy's innocent human inhabitants, and had never taken any actual _pleasure _in it. As much as he hated the Wraith, he acknowledged that, in a sense, they were fundamentally animals trying to survive; they fed out of necessity rather than for pleasure.

But this wasn't the Wraith he was dealing with here.

The Genii hadn't come to Atlantis because it was the only way they could survive; they had come simply because they wanted its technology for themselves.

Kolya had killed Elizabeth solely because he wanted to cause pain to his enemy rather than out of a need to feed for the sake of his survival (He might not _like _the fact that the Wraith did that, but at least most of them regarded feeding as something that was necessary rather than something they actively enjoyed doing).

Even if it meant that he would never see her again in whatever awaited them after this life- what he'd discovered about the Ancients' research on Ascension suggested that they'd felt that there _might _be other means of existing after death, but there was nothing concrete either way-, he was going to make sure that the Genii commander paid for what he had done.

As he hurried away from the fallen bodies of his opponents, heading for the nearest teleporter that would take him towards the central tower- right now his best chance seemed to be to weaken their numbers by forcing them to split up; he might be good but he wasn't going to go up against eight trained professionals unless he had no other choice-, he activated the Genii radio he'd taken from the first soldier he'd taken out and quickly turned it on, taking care to minimise the noise at his end. Right now he could use any tactical advantage he could get if he was going to defeat these… people… and avenge Elizabeth's death; Sumner and McKay were still Kolya's hostages and under guard, which made it vital for him to have all the information he could if the expedition was going to get out of here with _any _of its senior staff alive (As much as Sumner and McKay might get on his nerves- Sumner for trying to capture him and McKay for his arrogance-, he had to admit that they _were _good at their jobs).

"_Commander_?" a voice said over the radio, prompting him to stop as he listened to the conversation.

"_Yes, Sora_?" Kolya replied (He filed the name away for future reference; 'Sora', if he recalled what he'd gathered from listening in on mission briefings correctly, was the Genii woman whose father had died during the attempt to infiltrate the hive ship).

"_Laden has been leading three of our men on a reconnaissance mission_," Sora continued, frustration mingled with regret in her voice. "_It seems that the Phan- the _blasphemer_- has killed three more of our strike team_."

He didn't even feel any guilt at the reminder that he had done more than just kill his opponents; right now, he was more intrigued at her initial reference to him as the Phantom before she 'corrected' herself.

If there was 'dissent' among the ranks of the Genii regarding their current actions, that might _just _make his attempts to take the city back easier…

"_Tell everyone to fall back to the control room_," Kolya's voice said, its tone clearly reflecting his barely-controlled hostility

"_Right away, sir_," Sora replied briskly; evidently she was grateful to have a reason to limit any further deaths that might take place.

After a brief pause, as though both sides of the conversation were contemplating their next decision, Kolya spoke again.

"_Radio Chief Cowen_," the Genii commander said grimly, in a tone that made it clear he had made his mind up regarding his next course of action. "_Tell them to send reinforcements; a full company_."

With that, the radio conversation ended- this time for definite; the sound of the connection being terminated was unmistakable, leaving the Phantom with a grim smirk on his face as he took in what he had just learned.

_Back-up's coming, hmmm?_ he thought to himself, his grip tightening on his gun as he turned his direction towards the gateroom. _Well, if they've come so far, it's only fair that I arrange the… proper reception… for them_.

Once again, the plan that he had just come up with would once have horrified him; he had long ago promised himself that, if he had to kill humans, he would only kill those who had actively done or had sought to do him harm, and not simply kill people just because they were working for somebody who had acted against him.

As it was, however, he only considered it just punishment; no matter how many Genii soldiers might be killed when they came through the Stargate, it couldn't cause them even a _fraction _of the pain that he had felt at the loss of Elizabeth.

_Just remember, Kolya_, he thought grimly as he turned his steps towards the control room, a plan already forming in his mind. _You brought this on yourself; I gave you the chance to leave this city peacefully, and you went and killed her_.

_For that alone, you deserve _everything _that is going to happen to you_…

For the moment, his plans for personal revenge against the Genii commander would have to wait; right now, his more immediate priority was to give the invading Genii forces even _more _power problems to worry about than just powering the shield. Even without the ZPM, the naquadah generators the expedition had set up to help limit the depletion rate of the ZPM- with only fifteen percent of its full power capacity remaining, the possibility of a Wraith attack hovering over them constantly and no way to recharge the module in question, using the generators to power what they could and cut back on the power the ZPM had to use only made sense- were providing the city with enough power to operate the essential systems, which meant that the Genii still had control of most of the city's systems.

With the possibility of the remaining jumper coming back to Atlantis at any time- assuming they'd even received his original message; he freely acknowledged that he had no way of knowing why they'd had to remain behind in the first place and they could just not be able to come and help out no matter how long he waited for them-, he had to give the Genii even _more_ to worry about that just his continued presence inside the city; his own presence might not set off the city's internal sensors, but if the jumper returned while the Genii still had access to full power than the crew would be captured almost instantly.

Quickly shifting direction, he turned and hurried towards the nearest generator- the one responsible for powering the main tower, if he recalled the schematics correctly; he'd needed to re-learn a few of his old routes though the tunnels after these things had been installed to ensure he didn't accidentally disrupt anything during his wanderings-, reaching it only a few minutes after he started.

Turning his Genii radio on once again- if he was going to cause problems for the Genii, he'd like confirmation that he was causing the _right _kind of problems-, he smiled grimly as he reached out to remove the central power core from the heart of the generator, grinning as he pocketed the core as the lights went down.

It might be darker than before, but he'd spent so long inside this city that he practically knew his way around with his eyes closed; the Genii, by contrast, would _not _have that advantage.

"_Commander_!" Sora's voice said over the radio. "_The… blasphemer… has cut power to the control room_!"

"_How_?" Kolya responded curtly; evidently his much-vaunted sense of superiority was taking some serious knocks as the situation grew increasingly out of control.

"_It looks like, in the absence of the 'Zero Point Module' that he extracted earlier, Atlantis is being powered by five small Generators, each responsible for a separate area of the city_," a third, as-yet-unknown voice replied, his tone sounding professional as he relayed the situation to his commander; if he hadn't been working with the people who'd killed Elizabeth, the Genii's unknown listener had the impression that he might have actually liked the guy, who at least struck him as _slightly _less arrogant than his colleagues. "_This… impostor… has apparently disabled the one generator that powers Stargate operations and this tower. We still have most primary operations…_"

He paused, evidently consulting something, before he sighed in frustration. "_We have definitely lost all secondary systems_."

As their unknown 'eavesdropper'- a childish term, but here he was listening in on other people's conversations; it was pretty much trademark eavesdropping when you got down to it- turned to hurry towards the nearest teleporter and begin the next phase of his plan.

If he was going to… persuade… the Genii to abandon Atlantis, they _had _to be convinced that staying behind wouldn't accomplish _anything _but getting themselves killed, which meant that the power supply for the grounding station where Kolya had taken McKay and Sumner would have to be his _next _target…

"_If you are telling the truth and we have been unable to track him using the city's sensors so far, why has he done this_?" Kolya's voice asked over his stolen radio as the listener headed towards the teleporter. "_Does the Stargate still work_?"

"_It's one of the primary systems; we can still dial out if we have to_," the unknown voice replied; for a brief moment, the listener hoped that he would suggest they depart, but he simply fell silent after relaying the relevant information.

"_Is the control room secure_?" Kolya asked as their adversary reached the teleporter, stepping inside it and selecting the necessary location on the displayed 'map' of Atlantis.

"_Yes, Commander_," Sora replied. "_I suggest we send some men to guard the remaining generators_."

"_No; he's trying to divide us into manageable numbers_," Kolya replied, as their silent eavesdropper activated the teleporter and then began to hurry towards the second naquadah generator; he could never quite understand how the teleporters could do that without any discernable transition time, but he _definitely _loved it. "_Just close Stargate operations until the reinforcements arrive_."

"_Understood_," Sora replied briefly- her voice sounded almost dejected; could it be that she was beginning to realise that she was in _way _over her head?-, before the conversation ended once again.

He spared no further thought for the Genii beyond keeping an eye on his Life Signs Detector to confirm the absence of any of his enemies in his immediate vicinity; for the moment, his goal was simply to shut down the naquadah generator powering the remaining grounding station. He was certain that Kolya wouldn't have Sumner or McKay killed so long as there was a chance of gaining control of the city- with Elizabeth… gone… only Sumner had the necessary command codes to grant Kolya full access to Atlantis, and McKay was the only man alive who understood enough about the Ancient technology in the city to get that shield up-, which meant that he was free to take that generator out of the picture for the moment.

As soon as he had reached and removed the power core from the second naquadah generator- rendering the grounding station control useless while still allowing the station itself to funnel lightning through-, he only had to wait a couple of seconds before he heard the unknown voice speaking over the radio again.

"_Commander_," the voice said, "_the intruder has just disabled another generator_."

"Yes Laden," Kolya replied- simultaneously providing the listener with the name of the unknown Genii-, "we're aware of that; he's cut the power to grounding station three!"

_And I'll do more than _that _before this is over_… the 'intruder'- and what right did these people have calling _him _the intruder; even if he'd been a member of the expedition, he'd still have been here before them- mused, as he turned around and began to head back towards the teleporter, his ear to the radio before it finally activated once again.

"_Commander_," Sora's voice said after a few moments of walking, her tone now urgent, rushed, and almost panicked, "_the storm has not slowed its pace; we have little time to get the shields activated- we should re-evaluate our goal, perhaps_?"

"_We still have more than enough time to complete our objectives_," Kolya replied, evidently still unwilling to give up his attempt to control the city; their opponent was starting to wonder if Kolya was even unable to accept the possibility of _failure_ as well as the possibility that he was wrong about something.

"_Then I must strongly advise that we send men down to repair the deactivated generators and to guard the remaining active ones_," Sora continued, her voice keenly reflecting her fear at the current situation; he wondered how many more problems she could take before she finally decided to accept defeat.

"_Agreed_," Kolya replied promptly to Sora's suggestion. "_Teams of two, but I want you and Laden to watch over the control room; as soon as the reinforcements arrive, have them take the blasphemer with overwhelming force_."

If it hadn't been for the fact that it would give away the fact that he'd been listening, the Phantom would have laughed.

_Just _what he'd wanted; with only two people remaining in the control room, it would be _child's _play for him to accomplish his main goal.

All he had to do was get to the main tower, hide in his usual observation point above the control room, wait for the Genii reinforcements to arrive, and then…

He allowed himself a brief chuckle as he turned the radio off.

It still wouldn't make Kolya feel all of the pain he'd felt when he'd heard that Elizabeth was dead, but it would come _damn _close…

Plus, of course, if he timed it right, it could also be _very _demoralising…


	15. Dire News on the Doctor's Scene

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: I know I promised to reveal the Phantom's true identity by this point, but the chapter was becoming so long that I thought it best to break it in half and upload the first part now; I hope you like it, and I assure you that the next part of the story will be uploaded VERY soon

The Phantom of Atlantis

As the Stargate began to light up in the traditional manner that indicated an incoming wormhole, Sora glanced curiously over at Laden; with Kolya having already taken two soldiers with him to keep an eye on his prisoners, she and Laden had been forced to limit the gateroom's protection to just the two of them if the remaining generators were to be properly guarded.

"How many can we expect?" she asked, looking back at Laden.

"A full company; sixty or more," Laden replied, shaking his head slightly as he looked around the room at the city that was now only just visible outside the windows through the rain. "I don't know _how _we were expected to take a facility this size with any less…"

"It was _supposed _to be a raid to retrieve what was rightfully ours," Sora pointed out, trying not to dwell too much on that fact; she might object to Kolya's decision to chance their focus from simply retrieving the Wraith data device to trying to take the entire city, but now that they were in this position, she just had to deal with it.

As the Stargate finished dialling and the familiar 'exploding water' effect appeared before her, Sora briefly nodded at Laden as she walked down to join the newly-arriving soldiers.

"Secure the area," she said to the first small group of soldiers- five of them had already come through the Stargate, and doubtless more would be arriving soon- as they took in their surroundings. "Then I want you to spread-"

She froze mid-sentence as, just the next two soldiers began to walk through the Stargate, a thin blue shield of some kind suddenly appeared in front of the wormhole, causing the two men who had just been stepping through the wormhole to collapse to the ground. Sora only needed a brief glance to confirm that the shield had apparently sliced them almost exactly in half as they stepped through the Stargate, with each soldier missing a leg, an arm, and a sizable portion of their torsos, a perfectly even line demonstrating where the shield had separated what parts of them had already come through the Stargate from the parts that had yet to make it through the event horizon.

"By the Ancestors…" she said in horror, staring at the shield before them as brief glows accompanied the sound of what she knew without being told were people hitting the shield at the other end, her eyes constantly shifting between the severed bodies of the two Genii before her and the impacts on the shield that now covered the Stargate.

"As I informed your commander," a voice suddenly said from above her, "you should pray to the Wraith for salvation now; you and your people have forsaken all right to my protection by your actions here today."

Spinning around in the direction of the voice, Sora's eyes widened in shock as she saw the figure standing on the balcony connected to the control room; even if the dim light that remained after the generator had been shut down, the gleaming silver mask and long black cloak were unmistakeable.

The _Phantom_…

_NO_! Sora berated herself, as she glared coldly at the man before them. _He is _NOT _the Phantom; the Phantom would _never _do this to natives of this galaxy simply for trying to claim their right_!

"STOP HIM!" she yelled at the other soldiers, aiming her gun at the… _impostor_…and firing, only for the figure to turn around and vanish into another corridor connected to the control room. For a moment all Sora could think about was following him, but then she remembered the Genii still coming through the Stargate; right now she had a duty to save those men before they were lost as well.

"This is Sora!" she yelled desperately into her radio as she hurried up towards the control room, one of the new arrivals close behind her. "Stop sending the reinforcements; the Stargate shield has been raised!"

Whether her message didn't get through or it was simply too late at the other end to do anything about it, Sora didn't know; all that she knew for certain was that, even as she ran, more and more Genii were entering the Stargate on their homeworld, believing that they would soon be present in the city of the Ancestors, only to be destroyed by the shield before they could even set one foot in the city…

"Commander!" she yelled into her radio as she reached the control, instantly seeing Laden's unconscious body on the ground; she briefly wondered why the Phantom had only knocked him out rather than killing him outright, but decided that this wasn't the time to be concerned about that. "The blasphemer has raised the gate shield!"

"_Shut it down_!" Kolya's voice roared over the radio, as Sora desperately studied the control panel; she vaguely recalled Laden showing her the controls, but she'd been so caught up in the current situation that she hadn't really been paying attention to what he was showing her…

"I-I don't know how!" she said desperately, as she desperately tried to recall which button to press to raise the shield. "Laden is unconscious!"

Even as more and more Genii impacted against the shield, with no way of contacting the remaining forces on the other side to warn them about what had taken place, all that Sora could do was watch and prey that they would stop before the Stargate shut down…

* * *

As he ran through the city, his cloak flying behind him as he examined his gun's power cell- enough power left for a few kill-shots or just a few more stun blasts; he definitely wouldn't be blowing any holes in anything with this power level, and he didn't have the time to get a new cell before the storm hit Atlantis-, he refused to allow himself to think about what he had just done. He had killed over fifty Genii soldiers, he knew that- he'd overheard the latter part of Sora and Kolya's conversation where she mentioned how many men had made it through the Stargate-, but he also knew that he'd had no choice; if they'd all made it through the Stargate, they would have hunted him down and picked him off like an animal.

_And maybe an animal is all that I am now_…

He shook that thought off; self-analysis could wait until _after _he'd convinced Kolya to leave Atlantis.

Right now he had a long-overdue meeting with the Genii commander to get to….

The city might have lost its leader as a result of his inability to save her, but if he could help it, the people who'd killed her would _never _dwell in the city themselves.

"_Commander_," Sora's voice said over the radio that he had left active in case of overhearing anything useful. "_Laden thinks he can have the gate fixed_."

Admittedly, that news wasn't great- he'd been hoping to use the disabled Stargate as a bargaining tool; either leave Atlantis with nothing, or he'd leave the gate disabled and they'd _all _end up trashed by the storm- but at least that saved him having to go back and reactivate it himself.

"_Did Athor's son make it through the gate_?" Kolya suddenly asked, breaking his train of thought.

"_Excuse me_?" Sora replied.

"_His _name is Idos; did he make it?" Kolya responded, a slight hint of… was that _desperation _in his voice?

_Well well well_… the listener mused, as he reached towards the radio he'd taken from the first two Genii he'd taken out, what seemed like almost a lifetime ago. _Looks like things just got a _bit _more interesting_…

"_No, sir_," Sora replied.

With that news, the listener activated his own radio; maybe now that Kolya had evidently lost someone important to him, he would be able to make the man see that there was nothing to be gained by trying to hold Atlantis.

"Sorry about Idos, Kolya," he said, making sure to sound almost casual as he spoke; he had to give the impression of being _totally _in control if he was going to convince Kolya to leave Atlantis on his terms. "What was he to you; nephew, godson, protégé?"

After a moment's silence- Kolya evidently couldn't believe he had the nerve to talk directly to him like this-, he continued speaking, maintaining his casual, almost flippant tone. "Whatever his connection to you was, I _am _sorry it happened, but really, if you hadn't provoked me by attacking my city-"

"_This city belongs to the Genii, _blasphemer_; how DARE you use the Phantom's name to deprive us of our right_!" Kolya yelled over the radio; clearly he had yet to learn anything from his recent experiences. "_You are nothing but a coward who hides behind a legend_-"

"I have already _told _you who I am, commander; is it _my _fault that you don't believe me?" he countered, unable to stop a slight chuckle entering his voice as Kolya's yells were cut off mid-sentence. He knew that provoking the man might not be his smartest decision, but right now he wanted to make Kolya think about more about his chances of surviving a continued fight against the Phantom, and the best way he could think of accomplishing that was by making it clear that he had little regard for the Genii commander's abilities; if he treated the commander like he wasn't a threat, maybe the man would see sense and realise that he wasn't. "Not that it really matters, anyway; the last time I checked, the score is still sixty to three in my favour."

A part of him couldn't help but feel guilty at the ease with which he'd just reduced Elizabeth's death to nothing but a number- just one of the three members of the Atlantis expedition who'd fallen to the Genii commander's plans-, but he shook it off and returned his attention to the matter at hand; he'd grieve once those who'd killed her were dead.

"Just remember, Kolya; _I _was prepared to talk about this," he said, his voice once again cold as he continued down the stairs towards the grounding station. "_You're _the one who drove me to activate the shield; I was willing to try and negotiate with you before you tried to kill me."

For a moment there was silence as the Genii commander fumed on the other end of the line, before he finally spoke again.

"_There are two things wrong with your current strategy, _blasphemer!" he spat into the radio (At least, he _thought _it sounded like Kolya had spat into the radio; the weather he could hear over the radio made it hard for him to be sure).

"Constructive criticism is always appreciated, Commander," he replied nonchalantly. "What is your problem with my strategy?"

"_One_," Kolya replied bitterly. "_The assumption that I would believe you would rather destroy the city than let it fall to us… is childish_."

"If it would keep the Ancestors' legacy out of the hands of those who would abuse it, there is _nothing _I would not do, Commander," he countered. "Anything else?"

"_Two_," the Genii commander continued, as though he hadn't heard or didn't care about his immediate reply, "_if and when I determine Atlantis unsalvageable, Doctor Weir, Doctor McKay and Colonel Sumner become obsolete_."

He froze.

No…

There was _no way _that he'd just heard that…

Elizabeth _couldn't _be alive…

If she was…

He swallowed, trying to hold back the horrified scream that threatened to come from his lips at the other.

If she was alive, he'd just given her undeniable evidence that he was nothing more than the monster he'd always feared he'd become from his time in this galaxy…

"Elizabeth's alive?" he said, forgetting his old promise never to refer to her by her first name; right now he was took shaken at the news of her continued survival to bother himself with details like that.

"_Doctor McKay was able to make a strong case for keeping her alive_," Kolya replied, now with a somewhat satisfied tone in his voice; his adversary could almost curse himself at the way in which he'd unwittingly given the Genii commander even the slightest hint that Elizabeth meant more to him than just another member of the expedition.

"Let me talk to her," he countered, fighting to keep his resolve under control as he spoke into the radio. For a moment there was nothing but silence, and then, just as he was beginning to think that Kolya had lied to him again…

"_Hello_?" said the voice he'd been listening to for the past four months- and _God_, he wished that sounded less stalker-ish than it actually was-, evidently shaken by the current weather conditions but nevertheless clearly alive.

_Or was she_…?

He couldn't take the chance that Kolya was using a recording to trick him; he _had _to ask her something that only the two of them would know and that Kolya couldn't have predicted he'd ask.

"I told you it would work for you, didn't I?" he asked her; it wasn't perfect, but it was the best thing he could think of under the circumstances that could lead him to the truth.

"_You did_," Elizabeth replied, sounding like she was smiling slightly at the memory. "_Thank you for that; it's kept me safe so far_-"

"_What are you talking about_?" Kolya said sharply, cutting Elizabeth off as he held the radio up to his mouth once again.

"Just… a note I left her after her arrival; I told her that the city would work to keep her safe," he replied, hoping that Kolya bought the lie; he wasn't sure if Elizabeth actually had the Ancient shield device _on _her, but if she did and Kolya took it she'd be deprived of the only thing that left him feeling even _remotely _comfortable at the idea of not keeping a constant eye on her.

"_It would appear that you were wrong about _that," Kolya replied, once again sounding smug; most likely he perceived the 'failure' of that promise as further proof that the expedition didn't belong in Atlantis. "_Right now, we __have less than one hour until the storm hits full force; if the power is not returned to grounding station three within the next ten minutes, Doctor Weir dies_."

He hadn't thought it was possible for his blood to become any colder than it had been when he first heard the news that Elizabeth was dead, but when he heard that news he nearly screamed.

He _couldn't _lose her again… not after suddenly regaining her when he thought he'd lost her for good…

If it happened again…

He shuddered at the thought of what he might become in that situation.

"_Her death will buy you another five minutes_," Kolya continued, drawing his attention back to the matter at hand. "_After which, should the power still be out, Doctor McKay dies, followed by Colonel Sumner five minutes later; we will then leave with what we can, and the city will be destroyed_."

He didn't even bother to reply; there just wasn't enough time for him to say anything. Turning around, he hurried down the nearest flight of stairs, his mind already calculating the faster route back to the naquadah generator that powered the grounding station while simultaneously trying to ignore the part that reminded him about the likelihood of falling victim to 'Murphy's Law' in situations like this. The entire journey from the stairs to the generator was mostly uneventful- he had to duck into a side room to avoid being discovered by a Genii patrol at one point, but it was nothing significantly challenging-, until he found himself once again inside the room containing the naquadah generator responsible for providing power for grounding station three.

_Finally_, he thought, as he pulled out the power core for the naquadah generator; given that Kolya hadn't called him to tell him he'd failed- and he _would _call; that man couldn't resist any opportunity to assert his superiority over his foe-, Elizabeth must still be alive.

All he had to do, he reminded himself as he slipped his gun back into its holster, was reconnect the second power cable like _so_, put the power core back into the-

"Stop!" somebody yelled from behind him; as he heard footsteps enter the room from the corridor he'd just come by, he could have cursed himself for not looking to see if the guards he'd passed earlier had doubled back on themselves. Whether it was another attempt on Kolya's part to torture him, or simply Sora's order in an attempt to avenge the Genii he'd already killed, he didn't know and didn't care; all that mattered was that, if he didn't deal with them soon, his time would run out and…

_No_.

He wouldn't even _think _it; he couldn't cope with _that _again.

"Look," he said, trying not to sound impatient as he remained motionless, "your commander wanted me to turn this thing back on, and I would appreciate being given the opportunity to do so-"

"Silence, _blasphemer_," one of the soldiers spat at him, before a brief sound of motion occurred that was most likely the man raising his radio to his face. "Sora, we have him."

"_Keep him alive_," Sora's voice said over the radio (Which at least answered the question of who had sent these men). "_I'm on my way_."

_Great_… the Genii's new prisoner groaned, as the radio connection was terminated.

Right now, he had two choices; wait for Sora to get here and allow Elizabeth to die (_Again_!), or take these two out and then move on.

_The only question_, he mused to himself as he stood there, desperately going over his options in his mind, _is if I even _want _to see her alive…_

Would she even want to _talk _to him once she learned what he was capable of?

The men he had sliced apart with the shield…

The soldier whose arm he had shot off simply to question him…

How could someone like Elizabeth Weir _ever _want to… to be with someone who could do that?

Even as his heart ached at the thought, the storm outside drawing ever closer to destroying the place that had been his home for the last two decades of his life, that ever-traitorous part of his mind wouldn't stop asking him which he'd prefer; a world where he could never be with her because she was gone, or a world where she saw him for the animal he felt he had become?


	16. The Name Behind the Mask

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

Almost as soon as the thought of letting Elizabeth die had occurred to him, the man known to all as the Phantom felt like throwing up.

No matter whether or not Elizabeth never wanted to talk to him again after she learned what he had done to some of the Genii earlier- she couldn't care that he'd done it to 'avenge' her; the fact remained that she was simply too good a person to _ever _feel… that way… about someone who'd done what he'd done-, if the last few hours had taught him anything, it was simple; he would rather live in a world where Doctor Elizabeth Weir hated and loathed him than live in a world without her.

He _would _save her, no matter what the cost to his hopes of ever becoming as close to her as he wished; if he allowed her to die because it would be 'better' for him, how was he any different from Kolya?

All he could do to at least try and make up for his past actions was make sure to make it quick for his soon-to-be victims…

"I don't mean to be a bad prisoner," he said, flexing his left hand in preparation for what he was about to attempt, "but Kolya is going to kill somebody if I don't get this thing back on in time-"

"_Silence_," one of the Genii said, cutting him off mid-sentence. "You shall do nothing; your loss is merely just retribution for your own crimes against the Genii."

Sighing, the new prisoner simply remained silent, quickly counting out the remaining time in his head- he had maybe a minute at most before Kolya shot Elizabeth for real-, swiftly coming to a decision about his next course of action.

"Well," he continued, raising one finger of the hand that held the naquadah power core in an inquiring manner even as he continued to hold his left hand up in the air, "even if I am not allowed to ask you to permit me to repair this generator, may I at least point out one flaw in your current strategy?"

"Which is?" one of the soldiers said from behind him.

With that, the man known to the Pegasus Galaxy as the Phantom stood up and, spinning around, thrust the knife that had been concealed in his left sleeve directly into the eye of one of the soldiers, following the attack up by a powerful kick to the other one's stomach that sent him to the ground, gasping desperately for air.

"_Never _assume that I do not have weapons on me," he said simply, staring grimly down at the fallen soldier before he picked up his gun and fired a quick 'kill-shot' at the man before him; he might have been forced to resort to less 'pleasant' measures to take out the other man, but that didn't mean he had to be brutal about it now.

Once again, the part of his mind that he spent so much time trying to deny taunted him with the knowledge that his more 'merciful' killings now didn't make up for what he'd done earlier, but he forced it aside; unlike last time, he hadn't taken them out in the most elaborate, brutal manner possible.

Besides, for the moment, he had more immediate matters to attend to than his guilt; specifically, making sure he didn't have a reason to feel any _more _guilty than he already did. Turning back to look at the naquadah generator before him once again, he quickly inserted the power core into its centre, smiling slightly as the generator lit up once again.

He'd done it.

The grounding station was once again at full power- and, more importantly, Elizabeth was still alive.

Now all he had to do was get back to the control room- if Kolya wanted McKay to raise the shield they'd _have _to go back there; it was the only place that wouldn't be a death-trap in the next few minutes-, take care of the remaining Genii- no more than ten, he was fairly sure; he might not have kept track of specific numbers, but he'd gathered a general impression of how many had come through the Stargate during the initial attack-, and then get to safety before Sumner could order his arrest.

_Not the _easiest _task I've ever set myself_, he mused, as he stepped back from the generator to admire his handiwork, _but not the hardest, either…_

"Put down your weapon and put your hands where I can see them!" a voice said from behind him, breaking his train of thought as he turned to find himself staring at the business end of a P-90 rifle, Lieutenant Aiden Ford standing at the other end of the weapon in question.

_Damnit_! he thought to himself, swiftly realising that the jumper that had been left on the mainland must have managed to get back to Atlantis in the last hour or so; he'd almost forgotten about them…

Just as he'd also forgotten, in his earlier desperation to call for help in fighting off the Genii, that not _everyone _on Atlantis was that appreciative of his continued presence inside the city; at the time he'd sent the message he'd been more concerned about getting extra manpower without remembering that, to some of the expedition members, he was regarded as almost as much of a threat as the Genii.

"Lieutenant Ford," he said, raising his hands as he looked patiently at the man before him- he'd made it a point to note the names of as many of the expedition members as he could, in the hope that it might remind them of his own individuality to refer to them by their names-, "I respect your desire to do your duty, but as you are no doubt aware judging by your presence here, we are currently facing a serious hostage situation down at Grounding Station Three and there is only a limited amount of time available-"

"We can _handle_ it; I'm already working on how to deal with the Genii," Ford stated simply, his eyes narrowing as he glared at the man before him, apparently unaware of Teyla Emmagen and Doctor Carson Beckett as they hurried up behind him. He noted with some relief that the new arrivals looked uncertainly between the two figures, clearly undecided about whose side they should actually take; evidently Beckett was another member of the expedition with a neutral opinion of the Phantom as an individual. "What we _can't _handle right now is a rogue element like you running around Atlantis and making it even harder for us to do our jobs; I don't know _what _you're trying to do here, but-"

Sighing inwardly at the lieutenant's evident stubbornness- he seemed like a decent enough person, but his loyalty to the chain of command to the point of nearly idolising his superiors meant that he was clearly willing to stick to Colonel Sumner's orders in this situation while seemingly ignoring the larger issue of the Genii army determined to take the city from its current inhabitants-, the Phantom sent up a brief apology to whoever might be listening before he swiftly kicked Ford's gun out of his hand. Almost before the lieutenant had even had time to realise that he was now unarmed, his 'opponent'- as much as the man didn't like thinking of himself like that; he considered himself an independent ally to the expedition rather than a threat- followed it up with a quick shot from his energy weapon that sent Ford collapsing to the floor.

"What the-?" Doctor Beckett began, looking in confusion between the two men.

"Lieutenant Ford is a military man by nature, but he is unfortunately the type of man whose way of looking at the world makes it hard for him to go against the orders of his superiors; I lacked the time necessary to convince him that it would be best to let me handle this my way rather than allow him to attempt to do things his way," he replied briefly as he looked at the Athosian woman and the Scottish doctor standing before him, slipping his gun into its usual holster under his cloak as he spoke. "I would prefer to be able to work _with _you two rather than have to stun you as well to save on the time I might waste arguing with you, but be assured; I _will _do it if I have to."

After a moment of silent inquiry had passed between the two of them, Teyla turned and nodded at the man before them.

"I assume you have a plan to deal with the Genii?" she asked, her controlled manner perfectly reflecting the reasons why she had led her people for so long prior to their meeting with the Atlantis expedition.

"I do," he replied, nodding briefly at the Athosian in thanks before he turned to address Beckett as well. "Doctor McKay, Colonel Sumner and Doctor Weir are currently being held in the control room by the remaining Genii- no more than ten of whom remain, if my calculations are correct-, who wish Doctor McKay to activate the shield. Given Atlantis's current power condition, he has decided to activate the shield by channelling energy from the lightning into the generators, thus negating the need to use the ZPM, after disabling the grounding stations to prevent the lightning being channelled into the ocean; the obvious downside, of course, is that the corridors of Atlantis will thus be filled with lightning as the resulting electricity channelled through the conduits-"

"Hold on; he's electrifying the entire _bloody city_?" Doctor Beckett cut in, staring incredulously at the masked man before him. "What kind of plan is _that_?"

"Doctor McKay's plan; he was determined to ensure that you retain access to the remaining power in the ZPM until you have no other choice _but _to use it," the other man replied briefly, before he continued. "On the positive side, the control room and Stargate operations- including the… gateship… bay will remain unaffected by the lightning; if you can reach the 'gateship' you arrived here in, you should be able to wait out the lightning safely enough."

"And what of you?" Teyla asked, looking inquiringly at the man who had single-handedly done so much to oppose the Wraith.

"What else?" he replied, smiling slightly as he picked up Ford's P-90, weighing it briefly in his hand before he slung it over his shoulder; with his weapon's power cell rapidly depleting, he'd just have to improvise and hope he knew enough about the gun to use it properly. "I'm rescuing the hostages; the second that Doctor McKay raises the shield, Kolya has no reason to keep him, Colonel Sumner and Doctor Weir alive."

"You will need-" Teyla began.

"_No_," he interrupted, looking pointedly at the Athosian woman as he indicated the unconscious form of Lieutenant Ford. "I need you to get him to safety- he might have tried to take me prisoner, but I at least know his _intentions _were good- and stay out of the corridors; I have a plan, and I need to do this alone. If I need a distraction, I will let you know what you are to do; otherwise, simply get to the gateships and remain there until the storm has passed. Understood?"

"Understood," Teyla confirmed, nodding in resignation- he knew Teyla's type well enough to know that she resented being ordered to stay out of the fight, but would accept his authority for the moment at least- before she turned to look at Doctor Beckett. "Hurry, Doctor Beckett; we doubtless do not have much time."

"Uh… right," Beckett said, still looking slightly dazed at everything that had just happened, but nevertheless apparently still willing to go along with what he'd just been told. "Um… good luck?"

"Thanks," the man in the mask replied, nodding briefly at the two members of the expedition as they picked up Ford's unconscious body, each of them slinging one of the lieutenant's arms over their shoulders before they began to hurry off towards the nearest teleporter.

For a moment, the Phantom simply stood in silence, listening to the ever-receding footsteps of the expedition members while he took the opportunity to go over his current 'strategy' one last time- admittedly, all he had at the moment was 'get to the gateroom and assess the situation', but it was still a _plan_- before he hurried off after them.

Right now, with time growing increasingly against him- by his calculations it was only a matter of minutes before the storm hit Atlantis with full force-, his only chance at doing anything was to reach the gateroom and do what he could to get Elizabeth and the other hostages out of harm's way before anything else happened.

As he finally reached the gateroom, he quickly took up his position underneath the balcony where the control room was located; from here he could listen in on the situation with the Genii while simultaneously avoiding attracting attention to himself. As he took up a position that would allow him to quickly target anyone coming down the stairs to the Stargate before they even realised he was there, his energy weapon in his left hand and his new weapon- he vaguely recalled that it was called a P-90- in the other, he couldn't help but clench his teeth in rage as he heard Kolya's voice yelling at someone to engage the shield; evidently the storm was approaching the point where Atlantis would either be shielded or shattered.

"I'm almost finished!" McKay yelled back, the Canadian scientist evidently feeling just as frustrated at this situation as the Genii did.

"A massive wave is approaching from the west!" the voice of the man he thought was called Laden yelled. "Without the shields-"

"McKay!" Kolya yelled in frustration

"We're starting to get hits on the Northern peer!" McKay responded. "Routing power to the corridor… now!"

For a moment, there was silence, and then McKay spoke again. "Now!"

Once again, there was a brief silence, followed by a third "Now!"

After another pause, McKay spoke once more. "OK, this is a problem!"

"What?" Kolya asked; if the situation had been less desperate, the listener would have almost taken pleasure in the sound of the Genii commander having lost his earlier arrogance.

"Look, I told you this was a long shot from the beginning!" the scientist yelled in frustration; the listener briefly wondered if Kolya would even remember what McKay had warned him about earlier, or simply- like the traditional image of the worst kind of scientists- disregard all data that didn't support his view of the situation they were currently dealing with.

"We already have serious flooding on the north and west piers!" Laden added (Their silent spy made a mental note to check those areas as soon as possible; he didn't immediately recall the Ancients leaving anything potentially dangerous over there, but with the expedition's attempts to capture him restricting him to the ventilation tunnels it wasn't like he'd had much reason recently to regularly go over the maps he'd made to remind himself of where _not_ to go in the city).

"It's no use!" McKay insisted desperately. "The city conduits just can't handle this kind of raw power!"

Whether McKay was attempting one last desperate gambit to drive the Genii out of Atlantis by making them think its destruction was inevitable, or he'd made a mistake somewhere in his preparations and power just wasn't getting through right, the listener wasn't sure; he'd studied the Ancient databases for years, and he knew for a factthat Atlantis _could_ cope with that kind of raw power, but it would still need to be channelled the right way…

"Is any power getting to the shield generator?" Sumner asked; as always, the expedition's military commander

"Nominal amounts; nowhere near enough!" McKay replied, fear and frustration evident as he responded to Sumner's statement.

"You said this would work," Kolya said to the scientist; if anything, the fact that he didn't yell this time only made the listener even more anxious about how the Genii commander would react to this latest problem.

"I don't know if you noticed or not," McKay replied, his patience with Kolya evidently wearing thin, "but _I'm an extremely arrogant man who tends to think all of his plans will work_!"

"Idiot!" Kolya yelled, his voice accompanied by the sound of something being hit; evidently he'd just fulfilled the dream of most of Atlantis's scientists and punched McKay.

"Hey!" Elizabeth yelled, evidently trying to spare McKay further punishment; he could have almost wept at this fresh proof that she was still alive- her voice now couldn't _possible _be a deception; she really _was _still among the living-, but forced his emotions under control.

When he'd saved her for certain, _then _he'd celebrate her survival; not before.

"This was a long shot at best!" Elizabeth continued, evidently determined to make the Genii see their point of view on this latest turn of events. "Why else would we evacuate the city? It was always our intention to dial out in case this didn't work!"

For a moment there was silence, as though Elizabeth was waiting to see how the Genii would respond to her statement, before she spoke again. "Within minutes, Atlantis will fail! You can leave and survive, or you can go down _with_ the city; you choose!"

For a moment there was further silence, the Genii frantically moving around the control room as they exchanged low comments with each other that the spy couldn't quite hear from his current position, before McKay spoke again.

"Look, it's no good; we're just not getting enough power to the shield generators!" he yelled; evidently he'd been trying to get around whatever was keeping him from activating the shields, but so far was having little luck.

"Are you really going to sacrifice the lives of all of your remaining men- _including _the information you might recover from the Wraith data device you just took back from us- on the off chance that this city _won't_ be completely destroyed by that storm?" Sumner asked; if the listener had been in a position to see what was happening above him, he wouldn't have been surprised to see Sumner glaring at Kolya as he tried to make his Genii counterpart see sense.

After a moment's silence- evidently Kolya considering what the colonel had just told him-, the Genii commander spoke again.

"Open the Stargate," he said briefly, evidently addressing the other Genii. "Start evacuating the remaining men."

"You're making the right decision-" Elizabeth began, as the sounds of people moving about in the control room reached the ears of their unknown observor.

"You're coming with us," Kolya interrupted, instantly ruining the brief hope in the listener's mind that he was dealing with a rational man; he just could _not _let old grudges die…

"What?" Sumner yelled, his tone reflecting an incredulity that matched his own.

"You will all serve the Genii as payment for what you've done," Kolya stated simply.

Once again, the Genii commander's adversary wished he had Kolya's throat within his reach; was this man even _capable _of acknowledging that he'd been in the wrong at _any _time? All the expedition had done was defend themselves from Kolya's attack, and he was acting like _they _were the people who'd committed the crime!

"For what _we've_ done?" McKay yelled, shortly before the sound of scuffling broke off any further conversation; evidently the Genii had decided to resort to physical action straight away and simply get out of Atlantis with what they could.

As the remaining few Genii came down the stairs, he smiled slightly as he noted that his calculations had been correct; there were indeed only around ten of them left, even with the small group of 'reinforcements' that Kolya had managed to bring through the Stargate earlier taken into account. The first two men- he recognised one of them as Ladon, much to his relief; that man had at least shown some respect for the prisoners while- he permitted to go through the Stargate unharmed, but as Elizabeth, McKay and Sumner began to walk past- McKay yelling about how this was a bad idea; evidently he objected to being taken prisoner like this-, he seized his chance.

Drawing his gun, he fired two quick stun blasts- all that his gun had the energy to accomplish with its current power cell- at Sumner and McKay to knock them out- the less awkward questions the better, and those two were large enough that it would be impractical at best for the Genii to try and carry them to use as hostages- before swiftly slipping the weapon into its traditional holster, pulling out one of the automatic weapons he'd taken from Atlantis's armoury earlier, and firing at the nearest two Genii.

It was barely even a fight; after training his reflexes in conflict with the nigh-on-superhuman Wraith, even with an unfamiliar gun in his hands, it was almost childishly easy for him to outdraw the only human-reflex-level Genii. Almost without thinking it, his gun had automatically targeted and shot at two of the remaining four standing Genii, both of them falling like stones as the bullets struck their heads.

It was when he turned to look at the eighth- the seventh had run for the Stargate while his attention was otherwise occupied- that his blood ran cold.

It was a man who could only be Commander Kolya- the arrogance of the worst kind of commander was obvious in his every motion; the moves of a man who was certain that any move he made would be the right one simply because he was the one making it- with a gun pointing directly at Elizabeth's head, her hair and jacket soaked from the rain.

"Let her go," he said coldly, raising the P-90 to point it at Kolya, his expression once again as cold as the mask that covered it.

* * *

Elizabeth was rapidly reaching the point where she was beginning to question her judgement on any Phantom-related matters; it was starting to seem like she just could _not _focus on anything else when that particular topic came up in some form or another.

Even with a gun pointing at her head and her captor dragging her back towards the Stargate, she still couldn't help but feel a slight thrill- whether from the tension of the situation or… something more… she couldn't be sure- as she stared at the man before her, his P-90- where had he acquired that from?- pointing at Kolya.

As she'd gathered from her past brief glimpses of him, the Phantom was dressed in a long black cloak that came down to below his knees, with black trousers and a black top on underneath it, and- from what she could see of his hands where he was holding the P-90- he was also wearing black gloves, with a holster containing a weapon that she couldn't quite identify strapped to his hip.

His most distinctive feature, however, was the silver mask that covered most of his face. Seemingly designed specifically for him, the mask's design was smooth and simple, with two small holes that were just large enough for the Phantom's eyes to be visible. It completely covered the upper part of his face- eyes, nose and forehead- while extending around the head to stop just over the ears, although how it remained attached Elizabeth couldn't guess. The curious thing about the mask was that the lower half of the face was drastically different; while it concealed the entirety of the upper half of the face, the Phantom's left cheek, the left side of his jaw, and most of his mouth were exposed, while his entire right cheek and the right corner of his mouth were hidden under the mask, which extended down to cover his chin.

"_You_…" Kolya growled, glaring at the man who stood between them as he continued to back towards the Stargate, rage evidently in his voice as he glared at the man before them.

"Me," the Phantom replied, his tone almost neutral as he aimed his gun at Kolya. "Now, I won't repeat myself twice; _let. Her. Go_."

Despite the fact that he had a gun pointing at him, Kolya actually seemed to chuckle as he tightened his grip on Elizabeth, his own gun still aiming at the Phantom.

"You wouldn't shoot me," he said, his arrogant confidence enough to make even the normally pacifistic Elizabeth wish she had an arm free that she could use to hit him. "You might hit Doctor Weir-"

"As I told her, _the city will protect her_," the Phantom stated simply, his eyes narrowing behind his mask as he stared at them. "I _will _shoot you if you don't let her go…"

As the two men continued to stare at each other, locked in a temporary stalemate, Elizabeth's eyes widened as she realised what the Phantom had just said.

Without ever letting Kolya know, he'd just told her _exactly _what she needed to do to get out of this situation…

Praying that she recalled the information from McKay's report on his later experiments with the shield device correctly- after the Phantom had drawn the shadow creature through the Stargate the Canadian scientist had carried out a couple of brief experiments with the shield device to see what else it could do while not leaving it on long enough to seriously drawn the power-, Elizabeth reached one hand into her inner jacket pocket to grasp the Ancient shield device she kept there; thankfully, Kolya had never bothered to search her, evidently concluding that, as a diplomat on her home territory, she would be unlikely to have had a gun available to her, and his attention was so focused on the Phantom now he barely even seemed to register what she was doing.

As the Genii commander moved ever closer towards the Stargate, Elizabeth slipped the shield device out of the inner pocket- she _knew _there was a reason she'd wanted to keep wearing this thing even when she was this wet-, and placed it against her shirt. As soon as the device had activated, Kolya's grip on her was lost as the shield automatically repelled the other individual; as McKay's experiments had confirmed, the shield could only protect one person, with any person making physical contact with the user being forced to release their grip when the shield was activated.

Before Kolya could respond to what had just taken place, the Phantom had fired at him, sending the Genii commander tumbling backwards through the Stargate while leaving her standing in front of the event horizon, staring shakily at the Stargate behind her as the wormhole shut down.

If she'd been just a few seconds slower…

"Doctor Weir?" a voice suddenly said, drawing her attention back to reality. Turning in the direction of the speaker, Elizabeth couldn't stop the brief jump as she saw the Phantom standing beside her, an unreadable expression on his face as he looked at her. "Are you all right?"

"N… no…" Elizabeth whispered, shaking her head as she reached up to turn her shield device off; she might be shaken at what had just happened, but with the immediate danger passed she had no desire to waste the shield device's power unless she had to.

"You will be," the Phantom said simply, taking one last brief glance at his surroundings before he turned around to look up at the control room. "Come on; we have a shield to activate."

It was only after the Phantom had already reached the control room that Elizabeth realised what he'd just said; shoving the shield device back into her pocket, she hurried up the stairs to join him.

"But… but _how _can you activate the shield?" she said, prompting the dark-cloaked figure to look up from the console that he had just been studying prior to her arrival. "I mean, Doctor McKay already failed-"

"McKay's good at what he does, I'll give him that, but I've lived in this city for the last couple of decades or so; do you really think I haven't worked out how to activate the shield myself by this point?" the Phantom replied, looking at her with what Elizabeth could almost swear was a smile under his mask before his expression turned grim as he reached up to his left ear, a quick tap with his fingers activating what she could only assume was a radio underneath or part of his mask. "Teyla, Doctor Beckett, are you all right?"

"_We are fine, Phantom_," Teyla's voice replied, her tone sounding somewhat grim over the radio (And Elizabeth was _not _jealous about the fact that the Phantom had apparently spoken to Teyla before he spoke to her; she was just… concerned about the woman who was rapidly becoming a friend to her making contact with an individual of fundamentally unknown motives, that was all). "_Doctor Beckett and I had a… close call… but we are within the gateship bay and Lieutenant Ford has been positioned inside the ship; you may activate the shield whenever you wish_."

"Good," the Phantom replied briefly, before he terminated the radio connection and turned his attention back to the matter at hand. "Right then; let's _do _this…"

Before Elizabeth could say anything else, the Phantom turned away from McKay's still-active laptop and began to press a couple of the controls on the Ancient console that the laptop was attached to (It only made sense that he'd use that, she supposed; the laptops might have been programmed to be compatible with Atlantis's systems, but if the Phantom had lived in this city for as long as the stories she'd heard from the Athosians suggested he was probably more comfortable with the Ancient way of doing things).

"What are you doing?" she asked, looking uncertainly at the Phantom.

"What McKay wasn't able to do; shutting down the emergency buffers attached to the lightning rods to enable the city to transfer the power to the shield generators," the Phantom said by way of explanation, rapidly moving crystals around on the console before him, his gaze intent as he carried out his work. "It's simple enough to turn them on again afterwards, of course, but turning them _off _isn't exactly straightforward; you need to disengage just the right protocols to allow the power to get through without letting in so much power that you fry the conduits…"

With that, he removed one last crystal from the console before he turned to smile at her, patting the console like it as a dog that had just performed a difficult trick. "Of course, once you know what you're doing, using the crystals like that is almost as simple as inserting slot A into hole B; you might find it hard to learn how to do it at first, but it's almost _impossible_ to forget once you have."

Before Elizabeth could ask him how he'd learned how to do that, the Phantom had already turned to look out of the nearest window, a grim expression on his face as he apparently took in the sight before him.

"Of course," he muttered, not even looking back in her direction as he spoke, "just because the controls to turn the shield _on _like that are simple to use, that doesn't mean the time factor should be overlooked in a situation like this…"

Looking out of the window herself, Elizabeth couldn't help but wince at the sight of the massive wave that was now approaching them, drawing closer and closer towards the outermost part of Atlantis with a speed that she would never have believed possible of something so large.

If she understood what the Phantom had just said correctly, then, even though the generators had been granted the ability to absorb the necessary power from the storm, they still needed time to gather enough energy to generate the shield in the first place; it wasn't exactly the kind of thing that could just be turned on and off at a moment's notice, after all.

Right now, unless the shield gathered enough energy in the next few seconds, Atlantis was almost _certainly _going to be shattered to pieces…

Then, as though it had always been there, the shield flickered into life, just as the wave was about to strike the outskirts of the city. As Elizabeth stared out of the windows, she could dimly see the awe-inspiring sight of the tsunami that had so nearly destroyed them breaking in half to sweep around the city's shield, leaving the city unharmed as lightning continued to strike the city' various assorted lightning rods.

The shield had been activated, the Genii had departed from the city with nothing but fallen soldiers and a practically useless raith data device to show for their efforts- as her team had already determined from analysing the data themselves, even if the ships were in the same places a recorded on the device there were just too many for the Genii to hit them _all _with nuclear weapons, and Atlantis itself had been saved.

Elizabeth almost couldn't believe it.

"We… we did it?" she said, turning to stare at the man standing at the control console, a small smile on his face under his mask.

"We did it," the man Elizabeth knew only as the Phantom confirmed, before he shrugged and indicated a nearby room, the smile fading from his face to leave a more professional appearance. "Well, I should probably be going now; my weapon's stun effect will be wearing off soon, and I somehow doubt that Colonel Sumner will be as… understanding about my presence as you are. Don't worry about the lightning getting me; I…"

He paused, as though uncertain if he should say what he was about to say, before he seemed to come to a decision. "I know a few places it can't get to; I'll be fine there until the storm's passed."

With that, the Phantom turned away from Elizabeth and headed towards the nearby room.

"_Wait_!" Elizabeth called, prompting the Phantom to turn back, the blackness of his cape merging with the shadows of the room behind him to give the impression that his mask was almost floating in mid-air.

"You've just saved the city…" she said, looking after him with an almost pleading expression; she somehow knew- most likely given his past habit of simply dropping in when needed and vanishing afterwards- that, once he walked through that door, she wouldn't be seeing the Phantom again until he wanted to see _her_. "You've saved _me_. Can…"

She took a deep breath to steady herself, forcing down the fear a part of her still felt after seeing the swift manner in which he had eliminated the Genii, before she spoke again. "Can you at least tell me your name?"

For a moment, as he turned back to look at her, the gleam of the silver mask caused by the city's dim lights and the flashes of lightning from the storm outside making the visible flesh of his left cheek seem darker in comparison, she thought that he was going to refuse to answer, or simply say "I am the Phantom" as he had said to Kolya during their earlier 'conversation' over the radio, rejecting her attempts to try and learn something about him as a _person _rather than as the _Phantom_…

"My name is John", the Phantom said as he stared at her, breaking into her train of thought.

With that brief statement, he turned around and continued to walk, his dark cloak vanishing into the darkened corridors leading away from the gateroom before Elizabeth had the opportunity to ask him any further questions.

As she stood there in the dimly-lit city, surrounded by the dead bodies of the Genii and the unconscious forms of Colonel Sumner and Doctor McKay, Elizabeth couldn't help but wish that he'd remained behind- and it wasn't just because she wanted to ask him for more information about himself.

Even without having actually spoken to him beyond the required exchange to learn what he was planning to do right now, even with the fact that his motives for acting to save the city from the Genii were still a mystery to her, even with the ruthless way in which he'd dispatched the Genii soldiers taken into account (Elizabeth had always known that war wasn't pleasant, but this was the first occasion where she'd directly witnessed soldiers in a combat situation)…

A part of her still wanted nothing more than to have the chance to talk to him face-to-face and learn more about him as a person rather than the legend she'd heard about already.

Elizabeth wasn't sure what disturbed her more; the fact that a man could cold-bloodedly shoot six men like that, or the fact that she was still at least somewhat interested in him even after watching him do it.

'_Somewhat' interested_? She thought to herself, even as she reached up to activate her radio and confirm that Teyla and Doctor Beckett were as safe as the Phantom had told her they were. _That's a bit of an understatement, Doctor Weir_…

Forcing the matter to the back of her mind, Elizabeth turned her attention back to the bodies around her, already trying to work out the best place to leave McKay and Sumner until they regained consciousness and the storm had passed.

Her thoughts about the Phantom- _John_- could wait; right now she had other things to deal with.

AN: Well, there we have it; the Phantom's real name- part of it, at least- has been revealed…

And yes, I know that it was pretty much OBVIOUS that the Phantom was really John Sheppard from the beginning, but I wanted to have at least SOME mystery in his character, and I still have to answer the more interesting questions of how he came to be in Atlantis over twenty years ago in the first place…

AN 2: Next chapter we jump a couple of weeks ahead to look at the aftermath of this particular experience for the expedition, as well as how it affects Elizabeth's interaction with the Phantom when Atlantis faces its _latest _threat (Hint; it's from one of the episodes)

AN 3: For anyone wondering what happened to Sora, she saw the Phantom talking with Beckett and Teyla in the grounding station control room, but didn't bother attacking them at the time because she was initially at a serious numerical disadvantage and then because she doubted her ability to defeat the Phantom after he had so easily eliminated most of the other members of the strike team despite being outnumbered; her final fate will be revealed in the next chapter, but I didn't see the point in writing about it here as it didn't impact on my main plot. As for the severed bodies of the Genii soldiers John killed by activating the shield JUST as they walked through the Stargate, Kolya had them taken through the Stargate earlier, so Elizabeth never saw _those _bodies (Which doesn't mean she won't learn about others…)


	17. Too Many Years Fighting Back Tears

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: To let you all know, this chapter takes place a couple of weeks after the events of "The Storm"/"The Eye", and approximately during the events of the trip to the Ancient satellite witnessed in "The Defiant One"… with some _crucial _differences, of course (You'll have to wait and see what they are). I was originally planning to jump straight to "Hot Zone", but it occurred to me that I needed a few more moments showing John and Elizabeth when they're _not _facing a crisis, so this seemed like the logical thing to do instead

The Phantom of Atlantis

It had been almost two weeks since the city had so narrowly survived a storm that would have easily gone down as the worst hurricane in existence if it had taken place on Earth, but Elizabeth was nevertheless left wondering if she'd suffered some kind of long-term concussion during the Genii invasion of Atlantis.

Even after Colonel Sumner's reconnaissance teams- sent out to survey any potential damage that the city had suffered as a result of the storm- had discovered the bodies of the Genii soldiers that had been killed by the Phantom- one with a missing arm that Doctor Beckett's analysis confirmed had been removed by some as-yet-unidentified energy weapon _before_ the victim had been killed-, leaving clear evidence that the man possessed a brutal nature that could almost be said to be worse than the Wraith- at least their actions could be excused by the need to survive, even if a truly humane race would have found an alternative means of survival than feeding off other sentient beings-, a part of Elizabeth still couldn't _help_ but think about the man she now thought of as 'John' when she was alone and had nothing else to occupy her time.

She _knew _that he clearly had a potentially dangerous violent nature- the state of some of the bodies he'd left behind him proved that if nothing else-, but, at the same time, she couldn't shake the way he'd acted around her when the two of them had been the only ones left conscious and the city had been nearly destroyed before he'd activated the shield. As well as that, there was his behaviour when dealing with Lieutenant Ford, Doctor Beckett and Teyla to take into account; although the Phantom had stunned the lieutenant rather than attempt to talk to him- something that Sumner clearly objected to-, the fact remained that he had still talked to them rather than trying to force them to do what he wanted. His motives might be uncertain, but so far Elizabeth hadn't seen any evidence that the Phantom meant them any harm; as far as she was concerned, the Phantom's actions so far were enough to earn him at least some kind of reprise from Sumner's attempts to search for him, even if she was reluctant to actually voice that belief in case she gave her military commander the wrong impression.

Elizabeth just wished that Sumner would stop focusing on how things could have gone _wrong _and instead look at how they had gone _right_ (She sometimes wondered if the fact that the Phantom had stunned him and left her conscious had something to do with it; even after she'd told him that the Phantom had simply needed her help to enter the command codes- she just hadn't felt… comfortable… revealing the Phantom's real name-, Sumner evidently still resented the fact that the Phantom had once again ignored his authority in military-related matters on Atlantis). Admittedly, the Phantom's plan to re-take the city had been risky- from what Kolya had said during his conversation with the Phantom after the grounding station had been shut down, it sounded like Kolya had told the Phantom that she'd been killed; if that didn't reinforce how things might have gone wrong she didn't know what did-, but Elizabeth had her doubts that Sumner could have come up with anything _less _risky that would have driven the Genii out of Atlantis.

Besides, in the end, both the Phantom's plan and McKay's plan had managed to work out without any apparent problem; actually _extracting _the ZPM during the lightning storm might not have been something that McKay had been planning to do, but it had deprived the Genii of a vital potential bargaining chip, and the situation had still been resolved with minimal damage to Atlantis. The ZPM- along with the relocated C4 explosives- had been discovered in the teleporter nearest to the control tower after the storm had ended; McKay speculated that the Phantom had put the objects in question in a kind of 'stasis', activating the teleporter to send them to a certain location after shutting the receiving teleporter down, leaving them essentially stored in the teleporter's 'memory' until the receiving end was activated (Much like Earth's Stargate, according to a story McKay had told them as an example of how the 'trick' had been accomplished, had once ended up holding Teal'c's pattern after the Stargate at the other end of the wormhole was damaged and shut down before Teal'c could rematerialise at their end, forcing them to resort to rather… complicated… measures to get Teal'c out; McKay had been rather reluctant to explain _how _that had happened for some reason, but nobody had seen any point in pressing the matter).

Once the ZPM had been reconnected and the C4 returned to the storage rooms, the rest of the expedition members and the Athosians had returned to Atlantis- thankfully unharmed; whether the Manarians didn't know about the Genii's failure and had simply been waiting for a signal or had learned about the failed invasion and decided to try and act as though they'd never known about it nobody knew or was bothered in finding out-, leaving them with little to do but try and recuperate in the aftermath of the Genii assault and find out if their presence had caused any damage that they should be aware of.

So far the worst damage that the scans had picked up was some flooding in the north and west piers before the shield had been activated, although the few Genii corpses they'd discovered so far hadn't been pleasant either; the lightning that had been channelled through the conduits had all but incinerated the bodies, leaving them in a state that was best described as 'extra crispy'. The most disturbing discovery was the body of a young woman in a Genii uniform, located somewhere in the corridors between the grounding station and the gateship bay (Elizabeth hadn't asked for information about the specific location where the body had been discovered, mostly because she didn't want to know); unlike the other Genii bodies, the autopsy Carson had carried out showed that the woman had still been alive when she'd been practically fried by the lightning.

As far as they could determine, the woman in question was Sora, the Genii soldier whose father had been killed by the Wraith during the joint Atlantis/Genii attempt to infiltrate a Wraith hive-ship; based on the body, it looked like she'd unfortunately been in the corridors when the lightning had first struck the lightning rods and been electrocuted when the power had been channelled through the conduits. The most likely explanation that anyone had been able to come up with for her presence was that she'd been attempting to ambush Teyla, but she'd fallen behind while Teyla and Doctor Beckett were heading for the gateship bay- Teyla had privately admitted to Elizabeth that she believed the presence of the Phantom had prompted Sora to hold back until she was sure she wouldn't have to confront him-, and the lightning had struck before she could get to safety.

It was a tragedy, of course, but at the same time there was nothing anybody could do about it; all they could do was move on from that and try and ensure that nothing like that happened again (Personally, Elizabeth hoped they wouldn't _have _to be in that position the next time that storm struck Atlantis; the sooner they found a new ZPM the better as far as she and the rest of the expedition were concerned). It left them in a difficult position with the rest of the Genii, of course- over seventy of their men had been killed while on Atlantis, while the expedition had escaped with only a couple of casualties-, but in all fairness that would probably have been the case even if they'd had a couple of 'hostages'. Besides, after this last encounter, Elizabeth was strongly disinclined to try and contact the Genii again, no matter how desperate the situation became; given how their last two encounters with that particular group had turned out, it was evident that they had little interest in ensuring the survival of nobody except themselves, regardless of who was hurt in the process. As far as Elizabeth could see, if the Atlantis expedition was ever going to hope to survive the Wraith's seemingly inevitable attack, their best chance was to learn how to use the Ancient technology that remained in the city, as well as discover any possible Ancient research facilities that might provide them with further clues to developing a defence against the Wraith.

Currently Colonel Sumner and Doctor McKay were investigating a recent discovery that one of the junior scientists- Doctor Brendan Gaul, Elizabeth recalled his name was- had made while studying the Ancient database; an abandoned Ancient defence satellite, apparently the only one left from a network of similar satellites that the Ancients had once used to help them defend Atlantis, located on the edge of the solar system where Atlantis was located. Accompanied by Doctor Abrams and Sergeant Markham- Abrams to provide another perspective on the discovery and Markham to pilot the gateship; Sumner had only insisted on accompanying them because, as military commander, he felt it important to be kept aware of any new information regarding Atlantis's defences-, McKay and the scientists had gone to look at the satellite in a gateship. They had recently transmitted a message informing Atlantis that they had arrived at the satellite, but no sooner had they begun to study it than they had picked up a Wraith distress call from a nearby planet, apparently from a ship that had apparently been shot down during the final siege of Atlantis.

Admittedly, the ship was probably out of date by now- ten thousand years was too long a time for there not to have been some _slight _changes in Wraith technology- but personally Elizabeth doubted that there had been too many 'upgrades'; given that the gateship's weapons had so far proven to still be effective against Wraith ships, it seemed likely to her that the Wraith wouldn't have bothered to work on improving their technology after the Ancients had been defeated. After all, from what she'd heard from Teyla's stories, the Wraith- much like the Goa'uld- tended to come down particularly hard on any planet that had reached a technological level that might even have a _chance _of rivalling the Wraith; why would they want to waste time trying to improve on what worked when they were already at the top of the Pegasus Galaxy's food chain? Even with the Phantom's actions over the last decade, Elizabeth doubted that the Phantom- _John_- had made enough of an impact on Wraith society to merit them attempting to upgrade. No matter how many Wraith ships he might have destroyed over the last few years, the fact remained that he was only one man going up against an entire species; from what she'd seen of the Wraith, they were so arrogant that they would probably be convinced that he couldn't do that much damage to them until they were actually facing him, and even then they'd most likely underestimate him until it was too late.

Actually, that raised a question she'd never considered before; how _did _the Wraith perceive the Phantom (Even though she knew his real name now, she found it easier to think of the Phantom as just 'the Phantom' when thinking about what he'd done in the galaxy; somehow, she thought of him as 'John' only when his actions more directly affected her, most likely to make it easier for her to think of him as the legend and the man simultaneously)? From what Teyla had told her, the Phantom had saved a significant number of planets from being culled by the Wraith, but she had no way of knowing whether it had been as significant a number as Teyla seemed to think it was- she'd never been able to provide Elizabeth with specifics about how many planets the Phantom had saved; most people were content just to know that he was there- or if it only represented a small amount of the planets that the Wraith had attacked and the planets where he'd never shown up had simply never had any survivors to tell the story.

Had the Phantom made enough of an impact on the Wraith to make even _them _take notice, or did they simply regard him as an annoyance up to the point where he proved that he was anything _but _something they could just dismiss out of hand… at which point it was probably already too late for them to do anything about it?

"Doctor Weir?" Doctor Grodin's voice suddenly said, causing her to look up inquiringly at him. "We've just received word from Gateship One; they're leaving the planet and wanted to fill us in on their discoveries."

"Right," Elizabeth said, stepping out from behind her desk and walking into the main control room- the gateship had told them after sending the transmission that the planet's atmosphere would make radio communication difficult-, nodding briefly at the technician currently sitting at the control panel as he turned to activate the radio. "This is Weir; what's the situation?"

"_We've completed our investigation of the crashed Wraith ship_," Colonel Sumner's voice said, his tone as neutral as ever, refusing to give Elizabeth any more information than was absolutely necessary for her to do her job. "_As far as Doctors McKay, Gaul and Abrams can determine, the ship was almost certainly shot down during the Wraith's final battle with the Ancients. The evidence suggests that it was a supply ship; there were minimal weapons on the vessel itself, but the interior was filled with various chambers like those used on Wraith hive ships to hold recently culled acquisitions before they're fed upon_-"

"_Yes, yes, all in all an interesting bit of information but not of any real benefit to us in terms of giving us information about their defensive weaknesses; just let me tell her the _interesting _bit now_?" McKay's voice suddenly cut in, the Canadian scientist evidently excited at the implications of whatever he'd discovered. "_While we were looking around the ship, we discovered a few Wraith corpses that looked like they had been fed upon- it would seem that the Wraith can drain life energy from each other as well as from humans-, but most of them look like they died a while ago; initially, the most likely theory is that the last Wraith standing ran out of food, but_…"

"'But'?" Elizabeth asked, wondering what the reason for McKay's current uncertainty was. "What is it?"

"_Well_," McKay continued, his voice clearly displaying his uncertainty about the discovery, "_the freshest Wraith corpse we found was in such good shape that the thing could only have been dead for a few years or so- according to Doctor Beckett's reports they take quite a long time to decay once they're actually dead; their ability to heal keeps the cells going long after the brain dies and cause the Wraith to apparently take a good few _decades _to even _start _to decay-, and it's pretty clear that _something _killed it deliberately_."

"You're sure it didn't just die of hunger?" Elizabeth asked, even as she contemplated the implications of that statement; could it be that the Phantom- _John_- had been to that planet at some point in the past and defeated a _Wraith _in a one-on-one confrontation? "You said yourself that all the other Wraith and humans on that ship were dead; maybe it just ran out of food and died before you got there-"

"_Given that its entire _head _has been cut off- along with both of its hands; they're all only lying a few feet away from the body-, I'd say it's pretty clear this thing _didn't _go because it hadn't fed in a while_," McKay replied, his tone evidently sounding annoyed at the implication that he might have made a mistake on the scale of what Elizabeth was implying. "_Trust me, Elizabeth; whoever- or _what_ever- took that Wraith out, they knew _exactly _what they were doing and- given the lack of any _other _body anywhere near that one- they knew just how to do it without getting killed themselves_."

"_In other words_," Sumner's voice added, his tone the same precise one that she was already coming to think of as Sumner's 'Phantom tone'- the tone of voice that he always used when discussing matters relating to the Phantom-, "_it would appear that, in light of new evidence, I need to upgrade the danger the Phantom could pose to this expedition_."

Elizabeth blinked, exchanging a brief, concerned glance with Doctor Grodin- after he had learned about the events of the Genii invasion and the Phantom's actions in the expedition's defence, the British man had admitted to Elizabeth that he was also beginning to have his doubts about the hunt for the Phantom- before she turned her attention back to the current conversation.

"Can I ask why this information in particular should change anything?" she asked, doing everything she could to sound neutral; given Sumner's repeatedly-stated dislike of the Phantom's independent status, she had a strong feeling that nothing she could say would be sufficient to make him change that opinion.

"_Doctor, assuming that the Phantom is the only person to have been in this system for the last couple of decades- which, given that there is literally no other inhabited planets in this system, would seem to be correct-, we have just discovered evidence to suggest that he is capable of surviving against a Wraith in what all evidence would suggest was hand-to-hand combat; I think it's safe to say that he's potentially far more dangerous than we could have expected_," Sumner stated, his tone now almost laced with a slight trace of contempt, as though he couldn't believe Elizabeth wasn't seeing the situation the way he was. "_He was potentially dangerous enough when all we thought he could do was control Ancient technology to an- according to all sources- significant degree, but when factoring in his possession of combat skills sufficient to take down a Wraith without any back-up and apparently no advanced weapons, as well as his attitude towards his enemies during the Genii invasion, it's becoming increasingly clear that we're dealing with a highly disturbed individual with a dangerous knowledge of combat_."

Elizabeth had nothing to say to that, so she simply remained silent.

"_Instruct the security teams to be ready for a briefing from me when I return to the city; Doctors McKay, Gaul and Abrams can study their research well enough without my presence now_," Sumner said briefly, before he terminated the connection, leaving Elizabeth staring at the console in thought even as she nodded at Grodin to alert the security teams like Sumner had requested.

She knew that Sumner's line of reasoning was fundamentally correct; the evidence of the Phantom's brutality against the Genii wasn't exactly the most comforting discovery she'd ever made, and their lack of knowledge about the man's final long-term plans failed to help his standing with the expedition as a whole. All they really knew for certain about him was that the man clearly had no qualms about resorting to any means necessary to get what he wanted (Elizabeth had a suspicion that he'd… injured- she refused to even think the word 'mutilated'; given that the injuries had apparently been caused relatively quickly, the context just didn't feel right to her-… had been attacked like that because he wanted information out of them), and could be almost frighteningly cold when confronting his enemies; the look in his eyes when he'd shot Kolya- as though he'd like nothing better than to tear the Genii commander limb from limb- would always stay with her.

So why, even after all that evidence was taken into account and the picture it created was presented to her- the picture of a violent, ruthless man that she knew she would normally have run away from if she'd ever encountered him back on Earth-, did she still feel this strange… _interest_ in him?

* * *

Unknown to even Elizabeth, the subject of her bleak thoughts was currently crouched above her, sitting in one of the tunnels he regularly used to travel around the city, a slightly grim smile on his face as he recalled the confrontation that Sumner and McKay's latest discovery had called to the forefront of his mind once again. It had been one of the first times he'd gone up against a Wraith in hand-to-hand combat- he'd spent some time working out, of course, but all his previous encounters had been long-range fights while he was in a jumper-, and hence one of those occasions that would always remain in his memory no matter what other strange and remarkable things happened in his life as he continued to travel throughout the Pegasus galaxy.

He'd discovered reference to the Ancient satellite in Atlantis's databanks and taken a jumper to investigate, and had just been about to depart the satellite- he'd been planning to take a more in-depth look, but the lack of a spacesuit or the Ancient equivalent meant that he was unable to do so- when he'd picked up the Wraith distress call. Deciding to take a look- while also arming himself with an Ancient energy pistol, along with a makeshift sword he'd forged in his spare time in case he ever needed to get up close with a Wraith in a fight-, he'd taken his jumper down to the planet, landing it a decent distance away from the Wraith ship- also activating the force field via a 'remote control'-like device he'd picked up in one of the labs, in case of any unexpected 'guests'- and subsequently entered the ship to investigate it.

He'd quickly discovered the ship's sole survivor- a Wraith who seemed to have been feeding on both the ship's human cargo _and _his fellows, keeping them in stasis until he needed them-, but had fortunately caught him some time after his last meal, when the sucker was at his weakest. The guy might have been the toughest Wraith on the ship, but he'd been stuck there for so long without any fresh food that his healing abilities had apparently 'worn down' by the time John came to the planet. Absorbing other Wraith rather than humans might have made him harder to put down than the average Wraith was- based on something he'd read in the Ancient database, something about Wraith metabolism caused their healing factor to be 'amplified' if they resorted to cannibalism-, but the lack of food for so long had left the guy a bit slow. All John had needed to do was stay back until he'd managed to use his sword to injure the thing's hands- he'd cut them off properly once he'd weakened it enough, of course; he had no way of knowing if death would stop the Wraith's body attempting to feed or if it would operate on instinct like a headless chicken that kept on running about-, subsequently decapitating the creature while it was temporarily out-of-focus from the pain.

It hadn't been as easy at it seemed when he looked back at it, of course- he'd come close more than once to being fed on; it was one of the reasons he'd started to wear his current 'costume', as the material he used it provided him with an extra layer that could prevent the Wraith from easily feeding on him-, but it had still marked the first occasion where he'd managed to overcome a Wraith in a one-on-one fight. He'd kept the sword as part of his regular off-world 'armoury' ever since, finding it a useful weapon in case he ever came face-to-face with a Wraith and his gun had run out of energy for some reason, but he always took care to stay in shape with it; he'd been lucky when facing the Wraith at that time, but his encounters with the Wraith over the years since had left him with the knowledge that he couldn't depend on luck constantly.

And speaking of important memories…

He sighed slightly, reaching into his pocket to pull out the makeshift calendar that he'd put together shortly after his arrival; it was getting a bit worn after all these years, but it had helped him to maintain some sense of chronology while he was alone, allowing him to keep track of important dates…

Such as today.

In many ways, today was the anniversary of the day that had simultaneously destroyed and made his life; if those incredible events that had taken place twenty years ago had never happened, he would have probably lived a more peaceful life than he had done for these last few years, but, at the same time, it would have been far less interesting…

Plus, of course, if he'd lived the life he would have lived without that experience, who was to say that he would have met _her_?

No matter what else had happened in his life, if it was the only way he could ever have met the most compassionate, caring, courageous woman he'd ever known, how could he _not _be grateful for what had happened?

It was why he always made it a point to take today off whenever it came around; no matter how bad the past year had been, a few hours spent with what he had left of the woman who had given his life the purpose that he had once believed he would never find somehow _always _managed to make him feel better about himself.

Satisfied that Atlantis could manage without him for the next few hours- with the expedition's current efforts focused on tracking down any damage done by the storm, there weren't any teams offworld at the moment, and the Wraith didn't even know where Atlantis actually _was _anyway-, he turned around and began to make his towards the one room in the city where he could always be sure of having privacy, due to the fact that he'd taken it off Atlantis's sensor grid years ago.

It hadn't been easy programming the room so that it would never be discovered, of course- it had taken the better part of three years' worth of 'spare time' just to work out how to re-wire it so that the power for the internal sensors was diverted to generating a low-level force field around the room instead, simultaneously protecting it from damage and preventing anyone even realising that it was there-, but, as he hurried through the small 'maze' of tunnels that would lead him to the room, he considered it worth the effort.

After all, if it wasn't for the individual whose mortal remains were kept within this room, he'd probably have been dead almost twenty years ago; since he couldn't give her any kind of _actual _burial due to his lack of knowledge about what she'd have preferred, keeping her in stasis like this until he had the chance to ask the only person who'd know for _certain _what she would have wanted only made sense.

After everything she'd done for the city- and, albeit unintentionally, after everything she'd done for _him_-, giving her that chance was the least he could do to thank her for saving them both.

As he finally reached the mall door that would grant him access to the room, he opened it as quickly as he could- the system unfortunately still registered his presence as he entered and exited the room, meaning that he had to be sure to be quick to avoid registering on the sensors as anything more than a glitch- before he dived into the room, the door closing behind him as soon as he'd entered.

After waiting a few seconds in case any alarms had been set off- if anything was triggered he'd have plenty of time to get out of there before somebody else managed to get there-, he automatically made his way towards the chair that he'd set up here long ago. As he sat down in the chair, he allowed himself a slightly indulgent smile as he saw the sight of the old woman lying in the stasis chamber before him; even after all the years since they'd first met, her presence continued to have a calming effect on him.

Her younger self might be more beautiful in the conventional sense- smooth skin, thick dark hair, a light in her eyes that grew more incredible whenever some new discovery was made or a new victory achieved, an inner strength that belied her pacifistic nature-, but the woman now lying before him had, in her own way, a certain timeless beauty to her that would always appeal to him. Maybe it was the white robe she wore and the way her long white hair lay against it- combined with the soft lighting in the room; he'd had to dim the power requirements for that system to the minimum necessary amount to allow him to see in order to limit the power being drawn by this part of the city-, giving her an almost ethereal, angelic quality about her…

_Or maybe_, he though to himself, as he reached out to lay a hand on the chamber, _I just see her as an angel because she _was _one to me_.

She might have waited over ten thousand years to save Atlantis…

But she'd also saved him when he'd been nothing more than a young boy with no clue what had happened to him, giving him a chance and a purpose that he would never have possessed without her.

How could she be anything _less _than an angel to him?

The age gap might have been ridiculous at the time they'd met, of course- coupled with the fact that he'd been too young to seriously think of girls like _that _back then-, but he'd known even then that there was something special about her; it had just taken him several years to realise just _what _that was and why it had affected him so much.

It was one reason he was glad thing had turned out the way they did; how many people could honestly say that they'd had the chance to be with their first…

_No_.

He wouldn't- _couldn't_- go there; after what he'd done to the Genii during their invasion, he barely even deserved to _think _that he might have a chance with her in… _that _sense of the word.

All he could do was hope that he could at least see him as a friend, even if he could never forgive the brutality of his actions back then.

"Hi, Elizabeth," he said at last, his voice the same low tone that he always used when he spoke to her. It might have been a strange habit, but when half the population of the galaxy he was in wanted him dead and the other half would freak out if he simply unmasked in their presence, the body before him had quickly become the closest thing he had in his situation to a confidant. "Sorry I haven't been here much lately, but, well…"

He smiled slightly at her. "The expedition came through the Stargate."

After a moment's pause- he always liked to wait a few seconds in a situation like this; even with the Ancients' vague research on the topic, he didn't know if there _was _an afterlife, but he liked to pretend that, if there was, the older Elizabeth was listening to him and 'responding' in some way-, he continued. "They're all just as you described them, you'll be glad to know; apart from the detail of the city _not _flooding this time around, history seems to have gone exactly the same way it did before."

For a short while he simply sat in silence, looking reflectively at the still form before him, before he spoke again. "You… the _other _you…"

He sighed. "She's… she's everything you worried you couldn't manage to be; you'd be proud to see how far she's come."

He still recalled their brief conversations before the old woman before him had died; given that they'd been the last truly friendly conversations he'd have for over twenty years, it would have been impossible for them _not _to leave a lasting impression on him.

After she'd told him what little she could about the challenges that would face him once he began to travel to the rest of the Pegasus Galaxy- while simultaneously making him promise her that he wouldn't even _think _about going through the Stargate until he was certain that he could defend himself-, she'd spent her last few hours talking to him about more personal matters… including her own personal fear that, even if the expedition _had _managed to survive their arrival in Atlantis, she would have failed to lead them against the Wraith when they encountered the vampire-like race for the first time. He'd tried to assure her that, in his opinion, she would have done a great job at holding the city together- given how far she'd gone to save it, his young mind hadn't been able to conceive even the _possibility _that she wouldn't do just as good a job at running the city as she'd done when saving it-, but his youth had been against him and he'd been unable to present her with a convincing argument in her last few hours.

If he'd had that time over again…

He shook that particular thought off as quickly as he could; he'd already managed to get _one _second chance with her already, and the odds of getting that one alone had been so high that it was almost ridiculous to think about.

He'd come here for a few moments of peace; he wouldn't ruin that by thinking of what he might have said or done differently to make the woman now lying before him feel better in her last moments.

She'd died as satisfied as she could given the circumstances, her last words being to wish him well in the new life that he would now have to create for himself; all he could do was live that life to the best of his abilities with the aid of what she had managed to teach him, while simultaneously fulfilling his personal promise to protect her younger self when she finally arrived on Atlantis.

Even if her younger self could never feel for him what he had felt for her for almost as long as he had been in Atlantis…

_No_! he berated himself, fighting to halt that thought before it could much further.

That old dream didn't matter.

_Nothing _mattered except that she stayed alive, living the life that her other self had never had the chance to have herself.

After everything he'd had to do over the years since he'd arrived here, he'd long ago accepted the fact that his dream would remain simply a dream; the fact that he'd blown it before he'd had the chance to even _try _and have a few… moments… with her was just one of those things that sometimes happened.

He'd done terrible things to guarantee Atlantis's continued survival- as well as the safety of several planets less capable of defending themselves-; the fact that they'd been done for the best of reasons in no ay excused the brutality of the acts in question.

Even if she could ever understand his reasons, she could _never _bring herself to be with someone who could do something like that; she was too good a person to allow herself to 'sink' that low as to be with such a monster…

He had long since accept that; it didn't matter any more.

Only her safety mattered.

As far as he was concerned, everything else was secondary to that.

Only now, when he was alone and no dangers threatened the city that she had given her entire life to protect, in the room where his presence could definitively _never _be detected by any kind of outside clues, could he allow himself to be weak and feel the pain of that loss (If you could be said to lose something that you'd never really had in the first place)…

So he did.

For the first time since the expedition had come to Atlantis and Colonel Sumner had given the order to hunt him down before he endangered the city he had guarded for them, the man known to the Pegasus Galaxy as the Phantom lowered his head into his hands, and began to cry for the dream that had been ended by his own actions before it had really had a chance to begin.


	18. Nanites Unleashed

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Well, here's the "Hot Zone" chapter that I said I'd write, which will go on to mark the most significant shift in Elizabeth's 'relationship'- albeit a highly unconventional one- with the Phantom to date, as he finally begins to talk to her _directly_; hope you like it

AN 2: This chapter also marks the end of my use of "_Phantom of the Opera_"-inspired titles, as John begins to become 'John' rather than 'the Phantom' to Elizabeth (Just out of curiosity, I have two quick questions; 1: did anyone guess that was where I was getting my titles from, and 2: can anyone give me the original line on those cases where I 'tweaked' the line for the purposes of the plot?)

The Phantom of Atlantis

As she sat in her office going over the paperwork before her, Elizabeth couldn't help but allow herself a rare relaxed smile as she studied the latest reports from the various departments around the city.

So far, baring reports of flooding in the areas that had been hit by the waves before she and the Phantom-_John_; old habits really _were _hard to break- had managed to raise the shields, the news of the city's condition in the aftermath of the storm a couple of weeks was really surprisingly good. None of the rooms in the flooded part of the city appeared to have been significantly damaged by the waves that had struck them during the storm, and even the conduits themselves had come through more or less intact; the worst thing that any of the survey teams had discovered so far was a slight case of flooding in some of the more distant areas, and the water level barely came up to their ankles anyway.

At the moment McKay, Zelenka and Ford were walking through another flooded part of the city with an exploration team in an attempt to get a better idea of the damage that might have occurred- if any; so far nothing untoward had been detected in those parts of the city and a previous team had been through it and found no structural damage, but McKay had insisted on taking a second team in case there was anything of scientific value in that area -, leaving the rest of the staff to simply kill time according to their own preference. She vaguely recalled Sumner saying that he and Teyla were going to have a sparring session- after Teyla had taken out their one-time Wraith prisoner single-handedly Sumner had expressed an interest in learning how she'd accomplished such a feat, even if he was apparently still having some trouble mastering it-, while she had decided to take advantage of the temporary quite to study some of the reports she'd been receiving from the other departments; if anything, their access to a ZPM appeared to be creating far more work than she ever could have expected as ever more devices were activated by the expedition that apparently would have remained dormant without the module. Some of the science team were even hopeful that they'd stumbled across some information about creating- or at least 'refuelling'- ZPMs in one of their latest discoveries, but to date there had been nothing definite either way.

That was the problem with their research, really; the Ancient database was so vast, and their knowledge of the language so comparatively limited- once again she wished that the SGC had been able to spare Doctor Jackson for the expedition; his knowledge of Ancient was practically without equal-, that it made it hard to be sure if they had actually found something or if they were just getting over-excited by the few words they did know the meaning of in some files. Even the progress in finding the password for the shield that would stop it from preventing them from returning to Earth was still only making the bare minimum of progress; they'd managed to determine that the password was composed of anything between five or eight letters, but until they could actually find any clues to the specific word they were forced to resort to the process of entering every single possible Ancient word of that length that they could find until they'd identified the correct password.

If Elizabeth ever needed another reason to talk to the Phantom, there it was; the possibility that he'd be able to tell them the password to get back to Earth…

And why was it, even when she was fully aware that he had a brutal nature that left with little to no qualms about practically mutilating people to get what he wanted, she still wanted to talk to him; if any other person had demonstrated that kind of behaviour it would have horrified her…

"Doctor Weir?" one of the technicians said from her door, breaking into her train of thought as she glanced up from the file to look at him. "It's almost time for Doctor McKay's team to check in with the results of their survey; you wanted to be informed…"

"Thank you," Elizabeth replied, nodding briefly at the man as she stood up, picking up a pad with some of the forms on it as she walked out of the office; she just needed to confirm a few requisitions by some of the science departments for additional supplies.

"_Doctor Weir_?" McKay's voice said over the speaker just as she had walked up to stand beside the main control console; when he wanted to be the man could be surprisingly accurate at doing things on time, even if he sometimes complained about it. "_You there_?"

"Right here, Rodney; go ahead," Elizabeth replied; she had managed to get used to calling McKay 'Rodney' in public to encourage the informal attitude she wanted to establish in Atlantis, but Sumner's 'stick-to-the-rules-about-military-detachment' attitude meant that she found it easier to think of him as 'McKay' for when she was writing reports to prevent any 'slip-ups'. She trusted Sumner as a military commander, of course- his 'obsession' with getting rid of the Phantom aside, of course-, but given that they'd found themselves dealing with what was essentially a war situation, the less excuses she gave Sumner to question her ability to govern Atlantis under these conditions the better. "What's it like out there in the suburbs today?"

"_Essentially_," McKay replied casually, "_with the exception of the upper level Storage Room- which the lovely and talented Dumais informs me is in no immediate danger-_,"- Elizabeth couldn't help but smile slightly at that image; the idea of McKay _flirting_, even in that rather obvious manner that she'd just overheard, was somehow rather amusing-, "_this pier's in relatively good shape_."

"Even after all the flooding from the storm?" Elizabeth asked as she automatically signed her name on the forms before her.

"_Well_," McKay replied casually, "_it's dark, it's damp and it smells terrible, but from an engineering standpoint we're good_."

At that comment, Elizabeth allowed herself a slight smile of relief; after all the problems she was having to deal with the daily running of the city- to say nothing of her own internal issues on Phantom-related matters; if only she could finally work out _what _she felt for that man-, it was always a relief to have something simple to deal with.

"Head back," she said simply, as she finished signing the last form, passing it to the nearest technician to take to the necessary department heads.

"_Heading back_," McKay replied briefly before the radio cut out once again.

Shaking her head slightly at the latest report- it might have been uneventful, but the way things had been going recently a little peace and quiet was definitely not something to be sneezed at-, Elizabeth headed back towards her office; maybe now she could finally catch a few minutes' rest…

* * *

As Elizabeth walked back to her office, she was unaware of the silent observer watching her from the maintenance tunnels above the control room, ever determined to remain available in the event of a problem arising in Atlantis that might threaten its leader's safety.

In many ways, his recent 'visit' to Elizabeth's older self- he knew that, based on the story that Elizabeth had told him after he arrived, she was technically an _alternate _self of the Elizabeth he now knew rather than an older one, but it was simpler to think of her that way- had actually been rather cathartic; it had allowed him to get a lot of things off his chest that needed dealing with. The knowledge that he'd ruined his chance with Elizabeth due to the brutality of his actions during the invasion still hurt, of course, but at the same time the satisfaction he felt when he saw her still walking around Atlantis, knowing that he was the reason the city still had its leader, helped to make up for it.

When he'd originally made the promise to protect her, he'd done so out of respect and gratitude; the fact that things had… changed… for him since then didn't negate the fact that the original intentions behind him making the vow remained. He'd promised the older Elizabeth that he'd protect Atlantis for her younger self, and he'd done so; the fact that things were more… complicated… now didn't excuse him from his original vow.

Still, he was grateful that, for the moment at least, the city had nothing more to worry about than the usual problem of cracking the shield code that would allow them to dial Earth once again; after the chaos of the Genii's attempted invasion, it was really rather nice to have the opportunity to relax for a bit. With Sumner's teams currently checking out the more distant parts of the city in an attempt to find him- with him constantly changing his hiding-place and leaving little to no real sign of his presence in his 'abandoned' hide-outs, it was highly unlikely that they would ever manage to successfully track him down-, it was a rare moment when he felt comfortable enough simply relaxing in the main control room, allowing his attention to drift slightly as he looked out at the people who had brought life to this city where there had been nothing but himself and the ocean for the last twenty years…

"_Beckett_!" McKay's voice suddenly yelled over the radio, cutting into his train of thought; keeping his 'acquired'- _not _stolen; nobody had been using it- radio constantly tuned into a city-wide frequency might help him keep track of any important calls, but it was prone to be a bit startling on occasion. "_I need a medical team down here, stat_!"

That statement, almost more than the words themselves, instantly shook him out of his 'relaxation' mode and back into the 'Phantom' mindset.

_Why would a _medical _team be needed for a group carrying out a structural survey in _that _part of the city_? he thought to himself, slightly surprised at this latest turn of events. _I've been over that area already, and McKay just confirmed that nothing was seriously wrong; why would he want a _medical _team over there_?

Something didn't quite add up; McKay clearly wasn't in any pain _himself_, and that area was definitely structurally sound, so why was he asking for a _medical _team…?

"_McKay_," the familiar Scottish accent of Doctor Beckett suddenly said over the radio, his calm tone a welcome distraction from John's increasingly confused train of thought, "_this is Doctor Beckett. What exactly is the nature of the emergency_?"

"_It's too late_," McKay replied, his tone grim as he spoke. "_They're gone_."

John blinked in shock.

Someone- _two _someones, if hat McKay had just said was accurate- had actually _died _over there?

The situation had just become _far _worse than he'd originally expected; he'd been expecting someone to have been injured by a damaged wall at least…

"_Who's gone_?" Beckett asked; to his credit, his tone was brisk and direct, displaying no emotional reaction but instead sticking exclusively to the facts of the situation that was now before him. "_How_?"

"_Wagner and Johnson_," McKay said briefly by way of an explanation. "_I need a containment team here_."

"I'm sorry?" Beckett replied, clearly surprised at the request. For a moment John thought that he heard Lieutenant Ford's voice- most likely at McKay's end of the radio; he was fairly sure the lieutenant had joined McKay in carrying out the survey-, but then McKay began to speak again and his attention was called back to the scientist.

"_People don't just see things and drop dead, Lieutenant_," McKay was saying, evidently still slightly frustrated at whatever had just taken place down in that part of the city. "_We spent the last hour surveying unexplored areas of this city; I think Wagner and Johnson were exposed to something_."

For a moment John vaguely heard Lieutenant Ford's voice trying to say something, but then McKay interjected with a very pointed "_And_ if they were infected, _there's a very good chance that we were too_."

"_I recommend a Level Four quarantine until we know what we're dealing with_," Zelenka's voice suddenly said, the Czech scientist's statement far clearer than Ford's previous comments; either he was closer to McKay than Ford was or he was making a more deliberate effort to ensure that his voice was heard over the radio.

"_Agreed_," McKay said by way of confirmation. "_Carson, you hear all that_?"

"_Aye_," the Scottish doctor replied. "_We'll get to the hazmat gear and head down. Sit tight; I'll make sure Doctor Weir's briefed_."

"_Thank you very much_," McKay replied one last time before the radio connection was terminated, leaving the Phantom sitting silently in the tunnel as he contemplated this latest turn of events.

_A containment team needed in case they were… _exposed _to something_? John thought to himself, a confused eyebrow raised behind his mask as he went over what he knew of the experiments that he'd found records of in the Atlantis databanks over the years. _But the Ancients _never _experimented with biological warfare; after the mess they made with the Wraith they swore off _ever _trying something like that again, no matter how bad the situation got. The only thing that's even_close _to a biological weapon in the city is…_

He froze.

_Oh no… _he groaned, as the implications of this latest turn of events hit home. _Not _that_…_

He _knew _he should have moved that thing out of the city as soon as possible; why hadn't he _learnt _anything from that mess with Jinto after the young Athosian accidentally released that energy-sucking shadow? Just because there weren't any children on Atlantis any more after they'd all been relocated over to the mainland- Halling tended to alternate his time between his duties on Sergeant Bates' team and some time on the mainland with his son- didn't mean that some _adults _wouldn't accidentally trigger the systems!

Rationally, he knew that the current situation was far from being his _fault_; if nothing else, since the expedition had arrived in the city he'd had no opportunity to discard the nanites through the Stargate. Besides, he'd been too uncertain about how Sumner would have reacted to Elizabeth revealing that she was receiving information from the Phantom to risk letting them know that way; anything else he might have tried to fill them in on the problem was too subtle to be certain of success.

Besides, he'd never managed to determine a safe way of removing the containment devices from that room without releasing the nanites into the air at the same time, and even then he wasn't certain where he'd send them to once he actually reached the Stargate. Most of the things he'd discarded on abandoned planets during his time in Atlantis consisted mainly of the old plants that had been filling the corridors when he'd first arrived, along with some old Ancient experiments that either didn't work, had run out of power, or did nothing that he might be able to use against the Wraith (After all, he hardly wanted the _Wraith _to be able to use them against him if they'd discovered them). The risk that the Wraith would recover the nanites and find out a way to use them to make humans easier prey- maybe reconfigure them to simply render humans unconscious rather than trigger a stroke like they had originally- was just too great for him to risk it; at least when they were here he could make sure the nanites didn't cause any harm.

_So much for _that _little theory_… he groaned, as he glanced anxiously at his watch; he _definitely _needed to try and leave Elizabeth some kind of message about any other 'surprises' the city had to offer once he'd had the time to note down where everything was. Assuming he'd memorised the survey team's schedule correctly- and he accurately recalled the names of the deceased; 'Wagner' at least sounded unusual enough to stick in his memory-, he probably had just under an hour or so before someone else succumbed to the nanites that had been released.

That wasn't anywhere _near _enough time for McKay and his team to work out what they were dealing with. No matter how good they were at their jobs, they didn't know what they were dealing with and had no way of working out what it was based on their current minimal clues; somebody _was _going to die if they were left to work this out on their own.

If he wanted the expedition to have even a _chance _of getting through this latest mess without any casualties…

He swallowed, already anxious about what he was about to do.

He'd have to talk to Elizabeth directly, let her know what they were up against, and hope that she didn't just call Sumner and arrange for him to be sent into a trap for being a complete bastard with no regard for others…

God, if only he hadn't let his temper control him after Kolya had told him she was dead; he'd feel a _hell _of a lot more comfortable doing this if she _didn't _know what he was capable of at his worst…

"_May I have everyone's attention please_?" Elizabeth's voice suddenly said over the city-wide broadcast system, drawing his attention briefly off his own fears; maybe something had been discovered about the situation since he'd last heard a radio message. "_We have run into a questionable medical situation, and at Doctor Beckett's suggestion, we have decided to put the city into a self-regulated quarantine. For at least the next couple of hours, I need everyone to_ stay _where they are, and report anyone moving freely through the halls. I hope you'll understand. Thank you_."

John knew that the statement should have reassured him; they were aware of the situation and were taking every possible step to contain it to one part of the city rather than risk it spreading any further.

It didn't.

If anything, the words used only reminded him of just how much trouble he could be facing right now. If he didn't act _now _to let Elizabeth know what he was planning, then there was a very real chance that the city would initiate a lockdown and he'd be left with no chance whatsoever to solve this problem; the city even locked down the maintenance tunnels when quarantine defences were activated, and he wasn't exactly keen on keeping his shield device on for the time it would take to collect what he'd need, even if he'd been certain that it _would _stop the nanites from 'infecting' him.

Admittedly, his current plan for dealing with that particular problem was rather… vague, to say the least- he had no real idea what he was but if he could just have the chance to talk with Elizabeth and have her put him in touch with the right people, he was _certain _that he could get a better idea of the possibility of it being successful.

"Here goes nothing…" he mused, as he waited for a few seconds- since there was no reason for her to remain in the control room Elizabeth would probably head back to her office after making that announcement, which increased the possibility of him being able to talk to her without anyone else hearing him- before he turned on his own radio.

* * *

"_Doctor Weir_?" a shockingly familiar voice said in Elizabeth's ear just as she was sitting down behind her desk. "_Are you alone_?"

If Elizabeth hadn't already been sitting down, she was certain she would have fallen to the floor- or at least leaned against a wall- in shock at the sound she had just heard.

The Phantom was _talking _to her?

After spending the last few months in the city and only receiving a short note from him- during the Genii invasion he'd mainly been occupied with talking to Kolya rather than her, so she didn't exactly count that as him talking to her-, he was now _talking _to her?

Elizabeth wasn't sure whether to be glad at him finally breaking his apparent 'vow of silence'- in terms of the information he might be able to give them about the city; she was _not _an obsessed fan who wanted the chance to talk to her 'hero'-, or concerned about the fact that their current situation was serious enough to make him want to break his vow in the first place.

"_Hello_?" the Phantom- _John_, she reminded herself, _his name is John_- whispered again; Elizabeth had been so shocked at the unexpectedness of hearing his voice that she'd almost forgotten he was still waiting for a reply. "_Elizabeth, are you_-?"

"I'm here," Elizabeth replied, keeping her voice low as she glanced at her door; Sergeant Bates was standing just a short distance away from her office, but so long as she kept her voice low while talking she was confident she could carry on the current conversation without attracting attention. "As… interesting… as it is to hear from you again, we _do _have a situation right now-"

"_I am aware of that; I actually called to let you know what you're dealing with_," John replied, his tone sounding remarkably casual as he spoke, as though he wasn't talking to the leader of the people who were under orders to bring him in for questioning at the first chance they had.

"What we're-" Elizabeth began, before his meaning struck her. "You know about the virus?"

"_It's not a virus_," John replied simply.

Elizabeth blinked in confusion.

"Excuse me?" she asked, puzzled at the latest turn of events. "But two people have died without suffering any injury-"

"_I should rephrase that; it's not a _biological _virus_," John continued. "_It's artificial in origin; the deaths were caused by nanites that were part of the Ancients' last major weapon against the Wraith that were abandoned when the programming proved incomplete and the nanites were determined to be potentially dangerous to innocent parties_."

"Right…" Elizabeth said, unable to keep the uncertainty out of her voice. "Uh… assuming that I don't know what nanites _are_…"

"_They're microscopic robots that are used to complete specific tasks that their small size makes them ideal for_," John explained (Elizabeth was grateful that he didn't sound amused when he spoke; for some reason the thought of John thinking less of her was… unpleasant, for lack of a better term). "_No bigger than a conventional single-celled organism- less than a billionth of a millimetre, really-, __the virus is programmed to terrorise its victims by tapping into their visual cortex and then rupturing an artery in their brain, causing its victims as much terror as possible before their demise_. _They were designed to be unleashed on the Wraith as a last-resort weapon, __commonly inducing visions similar to those generated by the Wraith; I think the designers were the vindictive sort and wanted the _Wraith _to be on the receiving end of those 'visions' they're always using to terrify their victims for once. Unfortunate__ly, the programming the Ancients used to create this particular group of nanites- I've read some comments in the database which suggest that they made more later but I haven't managed to find anything conclusive - was inefficient; rather than just being deadly to the Wraith, the nanites were lethal to _everything _that wasn't an Ancient- or, at the very least, doesn't possess the Ancient gene in some form or another_."

Even with her admittedly limited knowledge of biology, Elizabeth shuddered.

That _definitely _didn't sound good…

Then she fully registered what John had just revealed to her.

"The _Ancients _made these things?" she yelled incredulously. "What were they _thinking_-?"

"_As I said, they made a mistake in the programming; it was intended to be a weapon against the Wraith, but in their desperation they activated the nanites before the programming was complete and they turned against anything that wasn't an Ancient_," John's voice replied. "_By the time they realised their mistake, they found it easier to simply contain the nanites in a near-abandoned part of the city rather than try and rewrite the code so completely; personally, I think they wanted to keep them around in the event of a 'Doomsday Scenario' in case the Wraith ever gained access to Atlantis and they had no other option but these nanites. There were some references in the database to them trying to create a new bunch of nanites later, but the information is all general and that's not really important right now; as far as I can determine that experiment was abandoned as well_."

"Right…" Elizabeth said, shaking her head slightly as she leaned back in her chair, trying to process everything that she'd just learned. "So… how does this help us deal with it?"

"_Well_," John replied, his tone solemn as he continued to speak, "_I _do _have a plan, but if I'm going to be able to confirm that it will accomplish my intended goal, I need to talk to Doctor McKay_."

Elizabeth blinked.

The Phantom was actually going to talk to someone _else_…?

And _God_, that sounded self-centred when she phrased it like that; she just _meant _that, after he'd spent so long only talking to _her_, it was strange to think of him being willing to talk to other people. It wasn't that she thought she was the only person he had a _right _to talk to, of course, but given that he'd only ever made contact with her- not counting his encounter with Teyla, Carson and Lieutenant Ford during the Genii invasion; on that occasion _they _had made contact with the _Phantom _rather than him going out of his way to find _them_- she felt somehow…

Elizabeth stopped herself right there; this was _not _the time to think about that!

"Why?" she asked, pushing any thoughts about her reaction to the Phantom's desire to speak to someone else aside; there would be time to give them a more in-depth analysis once this crisis was over.

"_I need to confirm the blast radius of the nuclear explosion that would result if I detonated a naquadah generator in the upper atmosphere_," John replied, his tone surprisingly matter-of-fact for such a statement.

Elizabeth's eyes widened at that last statement.

"You want to _what_?" she repeated, barely remembering to keep her voice down; the last thing she wanted was to attract the attention of Sergeant Bates during a conversation with Atlantis's 'Most Wanted'. "Are you even sure McKay won't… you know…?"

"_Try to trick me into handing myself over to Colonel Sumner_?" John replied, sounding almost amused by her concern. "_Don't worry about it; I already have a… pretty good idea how he'll react to me, I just need to let you know what I'm planning so that I don't accidentally wipe your hard drives when I set off the blast_."

"What 'blast' are you talking about?" Elizabeth asked, growing increasingly confused at the conversation she was having. "I mean, I may not have seen many nuclear explosions, but I wouldn't think that one in the upper atmosphere could have that much effect on us…"

"_The blast _itself_ won't; it's what _else _it causes that will solve the problem_…" the Phantom explained, sounding almost like he was smiling as he continued to speak. "_I can go over the fine details with McKay; I just need you to do _exactly _what I tell you and we should be able to get the expedition out of this alive without any more death_."

Elizabeth knew very well that, if Colonel Sumner had been present, he would have insisted on knowing more about the Phantom's plan.

But she was _not _Colonel Sumner; she was the leader of expedition, talking to the man who had apparently lived in the city for the last several years of his life, who had informed her that he had a plan that could save them from this… nanovirus… without any more death.

She might not know _everything _he was planning, but she had seen enough of him in action to know that what she knew was simply what she needed to know.

"All right," she said, settling back down into her chair as she kept her voice low. "What do you need?"

* * *

AN 3: If anyone wonders what I meant by that comment John made about the Ancients swearing off biological warfare after 'the mess they made of the Wraith', my reasoning is thus; since all the evidence we have available so far suggests that the Ancients played at least _some _role in the evolution of the Wraith, until we learn otherwise I'm assuming that the Wraith came about as part of an Ancient experiment that went wrong- my personal favourite idea is that they created the Wraith to be soldiers against the Ori but they lost control of the experiment for some reason and didn't realise what had happened until it was too late-, thus leaving the Ancients reluctant to resort to biological means of waging war in case they accidentally created something _worse _than the Wraith next time.

A bit of a stretch, I know, but I think it makes sense; I just don't want to say anything explicit as I'm trying to keep this as close to the 'real' series as possible- meaning that I'm changing nothing that took place prior to the Phantom's arrival on Atlantis- and don't want to contradict anything we might learn about the Wraith's origins as the show goes on


	19. It Might Sound More Than a Little Crazy

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Bonus points if anyone identifies the song where I got this title from (Chapter titles will now alternate between various lyrics from various songs that I feel reflect John and Elizabeth's relationship in this universe or whatever best describes the situation; one of my last reviews left me re-thinking my original thoughts regarding ceasing using song lyrics)

The Phantom of Atlantis

As McKay studied the information he'd managed to pull up on his laptop from the Ancient computers, he found himself liking the situation that he and his team had just stumbled into less and less with every passing second. Not only did they have to face the possibility that they were going to die of some horrible unidentified Ancient virus, but so far he wasn't having much luck in tracking down anything that they could actually _use _in the current situation. He might have been able to confirm that they were in an Ancient viral lab where the computer systems were cut off from the rest of the Ancient database, thus restricting them to hear if they wanted to learn more about the virus, but what they were actually dealing with was still a mystery to him; he didn't even know if the Ancients had _created _the viruses or were just studying them after finding them on some planet in this galaxy.

"OK," Zelenka's voice suddenly said from almost right behind him, breaking into McKay's train of thought as he studied the information he'd discovered so far on the screen before him. "I think that we…"

"Yes, yes, yes, yes, yes…" McKay interrupted, quickly running over what little of the conversation taking place behind him his subconscious mind had overheard- Zelenka, Ford and Dumais been talking about what container could have held the virus that killed Wagner and Johnson and expressed the possibility that the Ancient database could hold the answer about what kind of virus they were tackling-, before he continued. "It doesn't appear to be networked in with the rest of the Ancient systems-"

"_Doctor McKay_?" a voice suddenly said over his radio, cutting the Canadian off mid-sentence as he glanced down in surprise at the radio; he hadn't recognised the speaker's voice, and he'd assumed that he'd already met _everyone _in the expedition after spending the last few months in the city with few people to talk to apart from each other.

After a moment's confused hesitation, McKay shrugged and activated the radio.

"This is Doctor Rodney McKay; who is this?" he asked, noting from the confused expressions of the other scientists around him that they had no more of an idea about who was speaking right now than he did.

"_I am the Phantom_," the voice replied simply, a slightly amused tone in the voice as though the speaker found it rather amusing to say that line. "_I'm here to help_."

McKay blinked.

Whoever else he'd been expecting to contact him, he hadn't expected it to be _that _guy…

"Hold on; you're the _Phantom_?" he repeated, trying not to look as shocked as he knew he felt. "As in… _the _Phantom? The guy who took out that Genii invasion force a few weeks back?"

His eyes narrowed and his voice lowered as something else occurred to him. "The guy who _stunned _me while taking out the invasion force in question?"

"_The same_," the voice- the _Phantom's _voice- replied at the other end; unlike earlier, the speaker's tone now sounded almost embarrassed. "_On that topic, I would like to take this opportunity to apologise for stunning you like that; I had very little time available to me and could think of no other way to guarantee that the Genii would not continue to attempt to take you as a hostage other than rendering you unconscious and thus making you more difficult to move_-"

"I'm sorry, is that last comment meant to imply something?" McKay asked pointedly; if he'd been holding the radio the other people in the room had little doubt that he would have been glaring at it. "You know, a _weight _related something-"

"_This is _not _the time to argue about my opinion of your physical condition, Doctor McKay_," the Phantom's voice said, interrupting the Canadian scientist mid-sentence, the tone grim as he spoke. "_We have to get past that particular issue; if we don't act _quickly _then people will be dead in_-"

Before the Phantom could continue, the sound of someone whimpering audibly prompted McKay to turn around, his eyes widening in shock as he saw Dumais standing away from her laptop, her mouth wide open and her hands raised as she took deep, rapid breaths, an expression of terror on her face.

"Dumais?" McKay said, stepping forward slightly as he looked uncertainly at her. "Dumais? _Dumais_?"

Before he could say anything else, Dumais had turned to look in shock at Peterson, the other scientist standing in clearly-growing fear off to the side, and let out a small scream.

"It's all over you!" she screamed, before she rushed towards him, her hands desperately flailing all over his chest as though trying to brush something off his chest. McKay barely even registered Peterson's protests as Dumais continued to yell about something covering the other scientist; ignoring the Phantom's requests for information over the radio, he and Zelenka hurried over to pull Dumais off Peterson, only for the woman in question to clutch her head almost as soon as she'd been pulled away from the other scientist.

Before McKay could do more than remember that this was almost exactly what had happened to Johnson, Dumais let out a brief scream and collapsed to the ground, alternating between screaming and grunting as McKay and Zelenka lowered her to the ground, only to fall silent as they lay her down on the floor.

McKay didn't need to see the blood trickling from her ears and nose to know that she was dead; after the Genii invasion- to say nothing of that mess caused by the Hoffan drug-, he'd managed to get a very clear picture of what death looked like, and he was practically staring it in the face right now.

Staring grimly at the sight before him, McKay stood up, briefly shifting channels on his radio to send a quick message to Elizabeth.

"Tell Beckett to pick up the pace!" he yelled, unconcerned about manners; the situation was too serious to be concerned about minor social niceties like that. "I've just lost another member of my team!"

"Where's Peterson?" Ford's voice suddenly said, his tone low even as the words prompted McKay to glance up at his younger teammate.

"What?" he asked, almost hoping he'd heard the other man incorrectly.

"_Peterson_!" Ford replied, glaring back at McKay before he hurriedly walked over to the door, glancing briefly around the corridor before he turned back to look at the others. "He's gone!"

"_Let me guess; someone has run off_?" the Phantom asked; to McKay's relief- the Genii invasion had made it pretty clear to the Canadian scientist that he did _not _want this guy pissed at him-, the other man- or whatever he was; just because he _seemed _human from what brief glimpses they'd caught of him so far didn't mean he _was_- gave no indication of anger or frustration at being ignored like he had been earlier.

"_Yes_," McKay replied, turning his attention back to his radio, making no effort to conceal his frustration with the man on the other end; given that the guy wasn't angry at being ignored earlier, he felt slightly more comfortable at the idea of losing his temper at the man in question. "As you have oh-so-correctly assumed, one of my team _has _run off, potentially endangering this entire expedition if he _is _carrying this virus, and the _last _thing I need right now is _you _calling me to apologise for stunning me a _month _ago-"

"_I did not _just _call you to apologise about that; I called you because I know what you are dealing with_," the Phantom's voice cut in, sounding at least slightly frustrated at McKay's initial assumption about his reasons for calling the Canadian scientist.

McKay stopped yelling instantly.

"Excuse me?" he asked.

"_The 'virus', as you assumed it was, is actually a _nano_virus that was created by the Ancients as part of a plan for an anti-Wraith weapon that didn't work out like they'd hoped it would_," the Phantom continued, evidently refusing to give McKay a chance to interrupt him as he spoke. "_It was designed with the intention of being released into Wraith hive ships and attacking the Wraith on the cellular level- the theory being that the Wraith's natural ability to heal from pretty much anything would translate into an inability to cope with such 'attacks' due to their lack of medical technology rendering them unable to identify the nanites-, but the Ancients activated the nanites before the programming was complete; they'll kill anything that doesn't at least possess the Ancient gene around six hours after the initial exposure_-"

"Hold on; _six _hours?" Hays suddenly yelled, looking in shock at McKay in the absence of being able to look at the person who had actually told them this latest information. "But… but I ran into Dumais shortly after she met Wagner and Johnson!"

"Hey, I was _with _you-" McKay began.

"_As I recall, you underwent the Ancient gene therapy during your first few days in Atlantis, Doctor McKay; given that the nanites only target those without the gene, you will be perfectly safe_," the Phantom cut in, his voice slightly raised as he tried to call attention back to himself. "_However… Hays, correct_?"

"Uh… yeah," Hays replied, nodding slightly before he stopped himself as he remembered the person who'd asked the question wasn't in the room to see that part of his response.

"_Thank you… Hays, on the other hand, _will_ be dead in a short amount of time unless we can come up with a plan to shut the nanites down before that happens_," the Phantom continued. "_Tell me, Doctor McKay, would the EM pulse generated by detonating a naquadah generator in the upper atmosphere possess sufficient power to shut down the nanites without the explosion itself damaging Atlantis_?"

"Hold on; you want to _blow up _a naquadah generator?" Ford cut in, the sole military member of the group in the lab speaking up for the first time since the Phantom had first spoken. "You can't _do_ that; you don't have the authority-!"

"_In case you haven't been paying attention, _Lieutenant_, if I don't _try _it then you- the last time I checked you lack the Ancient gene- and at least a third of the population of this city face the very _real _possibility that you will all be dead within a matter of hours, particularly if Peterson makes it to a more populated part of Atlantis_," the Phantom countered, his voice cold as he spoke to the young military officer. "_You can either worry about how Colonel Sumner will react to the loss of a naquadah generator later, or suffer an aneurysm when the nanites that have almost certainly infected you by this point finish incubating and fulfil their pre-programmed function, thus rendering the issue of Sumner's reaction to my actions academic; the choice is yours_."

After a moment's silence as Ford considered what the Phantom had just said, the voice on the other end of the radio spoke once more. "_Shall I take your silence as meaning that you have acknowledged that I made a valid point_?"

"_Fine_…" the young lieutenant groaned, glaring pointedly at McKay in absence of being able to glare at the Phantom himself. "Just so you know, I _still _don't like this; you're an unpredictable element in a situation where we _need _stability-"

"_You don't have to _like _me, Ford; you just have to let me do what I have to do if this city's going to survive with most of its population intact_," the Phantom replied simply, before he turned back to McKay. "_Now, Doctor, getting back to the matter at hand; would the EMP generated by a naquadah generator being detonated in the upper atmosphere be sufficient to shut down the nanites, or wouldn't it_?"

"Well, given that their small size would probably translate into them being a _bit _more vulnerable to an EMP than conventional Ancient technology, I _suppose_ it's possible…" McKay replied, nodding thoughtfully before his eyes widened as he realised something. "Hold on; putting aside the fact that we only have a certain amount of generators, how the _Hell _are you meant to detonate a generator at the safe distance you'd need to be at to stop the radiation from hitting us just as much as the EMP?"

"_All I require from you is to direct me to a generator that you can spare; I'll do the rest_," the Phantom replied simply. "_Just tell me this; how high up would I need to be to prevent radiation from the blast damaging the city_?"

"Uh… twenty miles, give or take," McKay replied, looking over at Zelenka in a bemused manner that clearly demonstrated his own uncertainty at trusting the fate of the entire city to somebody they still knew relatively little about. "But look; if this goes wrong you could destroy our own computer equipment-"

"_If you have another plan that you _guarantee _will generate the necessary EMP, I'd like to hear it_," the Phantom countered briskly. "_Otherwise, let me do what I have to do, understand_?"

After a moment's quick thought- just in case he _could _come up with something safer in the time they had available to them-, McKay sighed and nodded in resignation.

"All _right_…" he groaned, looking in frustration at the radio. "Just… don't damage anything _else_ while you're doing that, will you?"

"_Of course not_," the Phantom replied, once again sounding slightly amused at the implication. "_Now, where's a decent generator for me to use_?"

* * *

A few minutes later, John found himself standing inside the jumper bay- he would _always _consider it the 'jumper' bay; 'gateship' just sounded so unimaginative to him (And that _wasn't _just the fact that he'd come up with it that prompted that opinion)-, a naquadah generator in his hands as he headed for the nearest jumper to his entrance tunnel. He'd managed to acquire the necessary generator quickly enough- McKay hadn't been able to just give him an inactive generator as the pulse would have taken too long to 'charge up' for detonation that way-, but he had been able to direct him to the generator currently responsible for powering the southern end of the city; as the least habited area of the city, disconnecting the generator from there would have the least amount of impact on the day-to-day activities of the expedition, particularly with the ZPM available to 'pick up the slack' until a new generator could be installed.

It hadn't been easy getting to this area, of course, but with Peterson currently occupied getting through the doors in the eastern part of the city, John had been able to save time by using the transporter to get to the southern end, recover the generator, and then transport to the central tower. So long as Peterson remained in that part of the city- which, with the transporters deactivated, would be his location for some time-, the city's damaged internal sensors couldn't detect the nanovirus and activate quarantine procedures, leaving power on in the rest of the city for John to travel from one part of Atlantis to the other.

He hated leaving the guy loose like that- there was always the possibility that he'd reach the control tower while he was otherwise occupied-, but he had to face facts; right now, the only thing he could do that could definitely help anyone was detonate the naquadah generator and hope that his and McKay's calculations were correct about the effect the blast would have on the nanites.

"Elizabeth?" he said, reaching up to activate his radio as he walked into the jumper, crouching down to activate the 'bomb hatch'- as he called it- where the generator could be placed and subsequently ejected when he reached the proper location above the city. If he understood the generator instructions correctly- and he was sure he had; after spending the last few years learning about Ancient technology by a combination of the Ancient database and trial and error, the generators were easy-, once he triggered the necessary overload, he would only have a few seconds to get out of the way before the thing blew up; he'd need to be fast when the time came…

"_John_?" Elizabeth replied, her voice low in his ear as she drew his attention back to the conversation at hand; he'd been so caught up in his thoughts about the generator's explosive potential that he'd almost forgotten that he'd contacted the Atlantis leader. "_What is it_?"

"I'm in the jum-the _gateship _bay-, and I'm just about to take the generator out to detonate it," he said, looking grimly around himself as he placed the generator in the hatch before he stood up and headed towards the cockpit. "You need to let the rest of the city know what's going to happen as soon as possible; when this thing goes off, the hard drive of every piece of Earth technology currently active will be wiped unless you shut them down."

"_Hold on; you _want _me to tell the rest of the expedition about this_?" Elizabeth asked, evidently surprised at the latest turn of events. "_The last time I checked at least _half _the expedition- mostly the military half, I admit, but there are definitely some civilians here who agree with them- would like to see you locked up_-"

"You _cannot _afford to lose _any _kind of technological advantage that might be gained by keeping those computer active; if that means I have to risk being captured, so be it," John replied, his tone direct as he activated the jumper and opened the outer hanger door that would take him out of the city. "If Sumner asks you how you know what I'm planning, tell him that I only contacted you to tell you to turn off your computers in order to prevent data loss; McKay and his group only know that I need to use a naquadah generator, but they don't know that I spoke to you before I contacted them."

"_What_?" Elizabeth asked, evidently confused at this sudden apparent change of topic. "_But if he knew that you were willing to _speak _to me_-"

"He would most likely try and have you removed from command for willingly engaging in conversation with a potential enemy of the city on the grounds that your judgement could have been compromised by your personal thoughts and feelings regarding my continued presence in Atlantis; I will _not_ allow you to risk your position on the chance that it might improve my own," John countered, his concentration equally divided between the conversation with Elizabeth and flying the jumper; it might have become second nature to him over the years, but a few months out of practice could make all the difference unless he paid close enough attention to what he was doing. "For the sake of the expedition, do _not _give him a reason to doubt you; simply say that I called you and told you what I was about to do before I turned off my radio, and you decided to go along with it just to make sure.

For a moment Elizabeth sat there in silence, most likely reflecting on what he'd just asked of her, before she sighed over the line.

"_All right_," she said, her tone making it clear that she wasn't sure about this but would respect his wishes nevertheless. "_If that's what you want me to tell him… that's what I'll tell him_."

"Thank you," John replied, allowing himself a slightly grateful smile- Atlantis needed a leader like Elizabeth if the expedition were going to make any allies in the Pegasus Galaxy- before another thought occurred to him. "Talking of capturing people, where's Peterson; McKay told me that he ran off, but I didn't gather anything else about what happened to him?"

"_He's still on the move, but so far we've managed to contain him in the eastern part of the city; the doors might only slow him down- apparently he has a good knowledge of Ancient technology-, but they're slowing him down enough to make a significant difference_," Elizabeth replied, her voice still low. "_John, are you _sure _about this_?_ I mean, what if the generator knocks out the gateship as well…_?"

"I'm sure," John replied, a grim expression on his face under his mask as he set a course that would take the jumper to a point high above Atlantis, forcing himself to ignore his relief at being in the air once again- it had been _way _too long since he'd been able to fly these things; it had been the first thing he'd ever discovered that he was _really _good at, and he still felt the same joy at being in the air that he'd felt when he first took one of them around the planet to scout it around- as he focused his mind on the task at hand. "This is the only way to be _sure _of saving the city; just give me a few minutes to get into position…"

* * *

"_You're trusting the _Phantom _to do something like _this?" Sumner's voice yelled as the control room staff around Elizabeth closed their laptops and disconnected them from the Ancient computers; she had no sooner issued a city-wide broadcast to alert the rest of the expedition to the fact that they were about to trigger an EMP before the colonel had contacted her from the gym where he and Teyla had been training before the quarantine began. "_Do you even _realise _how dangerous that could be, given how little we _know _about that man? Not only do we have no idea _why _he's doing all this, we don't even know that he's telling the truth about this virus; maybe it _is _just a biological infection_-"

"Doctor Beckett has already contacted me with the results of the autopsies his staff performed on the bodies of Wagner and Johnson; both of them were killed by a ruptured sacular brain aneurysm located in exactly the same part of the brain, directly above the visual cortex," Elizabeth interjected before Sumner could finish his rant; if he was going to accuse people of anything, she was going to make sure that he had all the facts available to him before he did so. "I'm not a medical doctor, but I think we can both agree that the odds of two different people suffering an aneurysm in the same part of their brain at the same time as the result of a biological infection are so remote that it's practically impossible for that means of death to have anything but an artificial cause, wouldn't you say?"

For a moment, Sumner was silent on the other end of the line, before he sighed in resignation.

"_All _right," he groaned, evidently unhappy about having to acknowledge that he would have to rely on the Phantom in order to save Atlantis. "_Just keep an eye on that gateship; I want a security team in the gateship bay as soon as this virus has been eliminated_."

"What?" Elizabeth said; she couldn't believe that, even at a time like this, Sumner couldn't stop focusing on his near-obsession with capturing the Phantom. "Colonel, if this is about your concerns regarding the Phantom taking action without consulting us, I'd like to point that he _did _inform Doctor McKay and myself what he was doing-"

"_We wouldn't even _need _his help if he had just told us that this virus was there in the first place_," Sumner coldly pointed out, his tone making it clear to Elizabeth that this was another occasion where no argument she could come up with would manage to convince him to change his mind (Or, at least, wouldn't allow her to change his mind in the time available before John's gateship landed). "_Even if he's been willing to consult with you before he took such significant action, if he'd just been less independent we wouldn't have to deal with this problem in the first place_."

"It's not like he did it on purpose-" Elizabeth began.

"_Purpose doesn't matter; the final results are all that I'm concerned with right now_," Sumner countered. "_In his own way, the Phantom's potentially as dangerous as the Wraith. We might know the Wraith's motives for culling other worlds, but we still have little to no idea what actually motivates the Phantom's actions, and his knowledge of the city could be dangerous if he ever decided to use it against us; hell, for all we know he could have released this virus _himself-"

"_Enough_," Elizabeth interjected; she might have promised John that she'd inform the city of the situation as though he'd only called her to tell her what he was doing rather than asking her if he could do it in the first place, but that didn't mean she had to allow Sumner to insult him like that. "I acknowledge that you have a point regarding our lack of knowledge about the Phantom's motives, but voicing unfound suspicions won't accomplish anything but creating paranoia in this city; I will _not _have your efforts to find the Phantom turn Atlantis into seventeenth-century Salem. Understood?"

"_Understood_," Sumner replied, a slightly hostile edge to his voice before he terminated the connection, leaving Elizabeth briefly worried that she might just have pushed her military commander slightly too far with the reference to the Salem Witch Trials. She knew that it might have been pushing her luck, but she'd honestly meant what she said; even if a part of her _could _see the value in Sumner's arguments about the Phantom's independence being potentially dangerous in the long run, if Sumner started thinking that the Phantom had done things when there was no proof that he'd had anything to do with them he was approaching the point where he'd have to be dismissed on the grounds of exaggerated paranoia.

Elizabeth didn't want to have to resort to that; as much as she and Sumner might clash on occasion about how best to run the city, he was the most qualified person to organise its defences in the event of the Wraith ever managing to find their way to Atlantis. John would do his best, of course, but he was only one man, to say nothing of being a man whom at least half of the military staff would like nothing better than to see out of the way…

And when had she come to depend on John for safety to _that _kind of extent? He may have saved the city from the Genii and that shadow creature- to say nothing of saving Sumner's team when they were trapped on the other side of that wormhole in the early days- but you could hardly get _used _to someone doing something after they'd only done it three times…

"_I'm almost in position_," John's voice suddenly said in her radio, breaking her train of thought as she turned her attention back to the more immediate matter of stopping the virus.

"I hear you," she replied, keeping her voice low as she slowly moved off towards her office; at least this way she wouldn't give any anti-Phantom members of the current control room staff any reason to further rquestion her ability to make decisions in that matter. "Would the EM pulse have any effect on the Gateship?"

"_The jum- the _gateship _is shielded from the effects of an EMP; it's the shockwave that concerns me right now_," John replied briefly.

For a moment Elizabeth simply stood silently off to the side, noting the deactivated equipment around the room- they'd done everything they could do protect their equipment short of actually sending it through the Stargate-, before she spoke again.

"Good luck," she said simply.

"_Thanks_," John replied briefly, before there was a brief crackle of static and he was suddenly broadcasting across what sounded like the city's public address system. "_Attention Atlantis, this is the Phantom. Ensure that all computers and electronic equipment has been deactivated; I am releasing the generator… _now!"

For a few seconds there was nothing but silence throughout the city- baring Doctor Grodin's voice as he counted down the seconds that followed the Phantom's statement, until, the moment Grodin said "One", the world outside the city windows was briefly illuminated in a brilliant white glow, so dazzling in intensity that everyone in the control room was forced to look away for the few seconds that the light lasted.

For a few moments, Elizabeth simply stood in the centre of the control room in silence, unwilling to try and contact John even as she wished she knew how he was- had he managed to escape the blast in time?-, before she finally heard his voice.

"_This is the Phantom_," he said, his tone neutral once again; evidently he didn't want to give away anything that would risk showing weakness given his official fugitive status. "The generator has detonated, and I have safely cleared the blast."

"Good," Elizabeth replied, privately satisfied with herself for choosing such a neutral expression; it could have been taken as meaning that she was glad the generator detonation had worked out as planned, or that she was glad the Phantom had escaped the resulting explosion.

As John terminated the connection- Elizabeth took that as a good sign regarding his faith in the plan; he was so certain that it had worked he felt no need to ask about it-, she turned to look at Grodin, who nodded as he activated the computer in front of him.

"_Just to make sure you know_," McKay's voice suddenly said from her radio, "_the pulse only lasts a couple of microseconds; once it's over_-"

"The computers are all fine, Rodney," Elizabeth said, smiling slightly as her staff around her moved to activate the various computers. "Once Doctor Beckett's checked you over to confirm that the nanites have deactivated, you have a green light to return."

With that said, she terminated that radio connection and turned to look at Sergeant Bates. "Bates, take a security team to Doctor Peterson's location; escort him to the medical wing if he needs more convincing that he is no longer infected."

"Understood," Bates said, nodding briefly at her before eh turned and hurried down the stairs, signalling to a couple of the surrounding marines. They had only just begun to advance towards the door leading to the corridors where Peterson had last been seen- Elizabeth hadn't had the chance to check the monitors to see where it was now-, when Sumner's voice suddenly cut in over the broadcast system.

"_This is Colonel Marshall Sumner_," he said, his voice making it clear that he expected his current orders to be instantly obeyed. "_All available security teams report to the gateship bay immediately; once the Phantom's gateship arrives keep all guns trained on it until my arrival_."

To Bates's credit, Elizabeth was gratified to note that he didn't automatically obey the order; he raised one hand to his ear to activate his radio even as he and his marines stopped walking. "Sorry, sir, but Doctor Weir ordered-"

Elizabeth couldn't hear Sumner's reply over the radio, but she was hardly surprised when Sumner's voice appeared on hers. "_I apologise for circumventing your authority, Doctor Weir, but Doctor Peterson can wait a few minutes; this is our best chance to apprehend the Phantom, and I will _not _allow him to slip through our fingers again_."

"Understood," Elizabeth replied briefly, terminating the connection as she turned to walk after Bates and the other marines.

Her issues with Sumner countermanding her like that would have to wait; right now, she had to make sure that any anti-Phantom soldiers with itchy trigger fingers didn't try to shoot John the second he tried to walk out of that gateship…

As Elizabeth walked into the gateship bay- taking care to keep a respectful distance behind the soldiers; she didn't want to appear overly anxious-, she glanced upwards just in time to see the gateship begin to descend into the bay as it entered through the currently-open hole in the roof, the ship already rotating to land in the only currently-empty slot in the entire bay…

It was only when the ship actually reached the ground, allowing Elizabeth and the marines before her to see through the cockpit window into the rest of the ship, that Elizabeth realised something she hadn't been expecting.

The gateship was empty.

Admittedly, it wasn't impossible to assume that John- the _Phantom_; she couldn't afford to risk slipping up and saying his real name at a time like this- was hiding somewhere in the ship where he couldn't be seen from the window, but she doubted it; what would he have to gain by attempting something that… well, _pathetic_? There was nowhere for him to go but out of the ship, and she doubted even Jo- _the Phantom_- could easily take out this many marines when they were all prepared and ready for him; his main advantage when fighting off the Genii had been surprise, which was something he'd only have a slight amount of here in relation to the amount he would have possessed during that confrontation.

Despite herself, as the marines stated in confusion at the empty ship before her, Elizabeth smiled.

She might still lack any knowledge about John's long-term motives, but she could say one thing for certain; since she'd learnt of his existence, her time in the Pegasus Galaxy had _never _been boring.

* * *

If anyone had been able to see the city from the outside at that point, they would have swiftly learned what had just taken place. Clinging to the highest part of Atlantis's central control tower, his long black cloak flapping in the wind as he looked down at the descent that awaited him, estimating the distance between here and the outer entrance to the emergency tunnels that he'd once discovered, was the black-clad form of the Phantom, a slight smile on his face as he listened to Sumner's shock over his radio.

_Sorry, Marshall_, he mused to himself as he began to climb down; in many ways, the Atlantis military commander's adherence to the rules made him almost worryingly predictable when presented with an opportunity like the one he'd almost been provided with. _But right now, I'm just not ready to sacrifice my independence; I can accomplish a _lot _more on my own at the moment_.

Maybe he'd make full contact with the expedition at some future date, but for the moment, he felt that he worked best 'undercover' in the event of something like the Genii invasion happening again; sometimes, a city like Atlantis _needed _somebody who was willing to go against authority and do what they _had_ to do rather than what they were _ordered _to do.

Until he felt that Atlantis had a commander who understood the value of that- much like what Elizabeth had told him about General O'Neill during their all-too-brief time together after he'd first arrived in the city; now _there _was a guy who knew that you couldn't win by sticking to the rules all the time- he'd risk getting in even _more _trouble if he made contact with Sumner than if he remained independent.

At least he was operating outside of the chain of command Sumner couldn't get _more _angry with him; if he even seriously _tried _to make an effort to work _under _Sumner- and it _would _be 'under'; he was sure of it- the two of them would end up fighting it out in a matter of days because John couldn't obey his orders…

As he finally reached the hatch that would allow him back into the maintenance tunnels, and thus into Atlantis itself, John shook his head as he opened the hatch before him.

He could worry about the future later.

Right now, his immediate priority was getting to a comfortable spot and having a decent sleep after his _latest _near-death experience (If having to set off a nuclear explosion and get away from it in thirty seconds wasn't a near-death experience, he didn't know what _was_).

* * *

AN 2: Well, the next chapter explores the aftermath of this particular escapade; I can assure you, Sumner and Elizabeth are going to have _words _next time around…

AN 3: If anyone's wondering how the jumper managed to land without anyone in it, I read somewhere that the jumpers apparently operate on automatic pilot when they're within a certain distance of Atlantis, hence explaining how Ford was able to use one to leave in "The Siege- Part Three" despite him lacking the Ancient gene. With that in mind, it seemed reasonable to assume that John would be able to set his jumper on autopilot once he drew in close enough to the city, subsequently jumping out the rear hatch and climbing down the tower from the outside while the security team kept an eye on things inside the gateship bay


	20. Meeting of the Managers

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

As Elizabeth sat in her office the next day, going over the various reports of what had taken place during the quarantine period, she couldn't stop herself letting out a brief sigh of relief as she confirmed that nothing serious had happened after Dumais' death. All members of McKay's team had been analysed by Doctor Beckett after his team had reached them, with their blood showing no trace of the nanovirus

The only member of the expedition with any long-term 'damage' as a result of the virus was Peterson; although the detonation of the naquadah generator had destroyed the nanites before the virus could do any physical damage, he had been ordered to undergo psychiatric evaluation with Doctor Heightmeyer to help him through his reaction to the virus. Elizabeth was currently thinking of relocating Peterson to a calmer area of Atlantis- maybe one of the jumper survey teams or something like that- until a more permanent solution presented itself, but so far nothing had immediately come to mind…

"Doctor Weir?" a voice said at the door.

Glancing up, Elizabeth wasn't surprised to see Colonel Sumner standing at the entrance to her office, a stern expression on his face as he looked at her.

"Yes, Colonel?" she asked, putting the reports she was reading off to the side as she looked up at her military commander. "What can I do for you?"

"We need to talk," Sumner said, his expression grim as he walked into her office, standing in front of her desk despite the chair that was positioned close to the desk. Elizabeth didn't need to be a diplomat to recognise what Sumner was doing by rejecting the chair; he was attempting to establish his control of the situation by assuming the 'higher position' in their discussion.

"All right," Elizabeth asked, looking coolly back at Sumner as she raised her hands in front of her, making it clear to the man before her that she wasn't intimidated by his actions. "What seems to be the problem?"

"Your attitude towards me regarding my opinion of the Phantom's plan," Sumner replied, his expression betraying nothing about his own feelings as he looked at her. "Your attempts to countermand my orders to the security team doesn't exactly give the impression that we're effectively establishing a chain of command-"

"Are you saying I'm not allowed to have personal opinions about the way this city is run?" Elizabeth countered, stepping up from her chair to look directly back at Sumner.

"What I _object _to is you voicing those opinions during that kind of public communication," Sumner countered, his arms folded. "It undermines the chain of command that's required if we're going to successfully operate in Atlantis, to say nothing of encouraging the idea that the Phantom might _not _be a threat; until we have any conclusive evidence that he's no danger to us, he should be treated as a potential threat at least-"

"I understand your position on the Phantom, Colonel; what _you _need to understand is that I will _not _accept you trying, whether intentionally or otherwise, to make him out to be a greater threat than he actually _is_," Elizabeth interjected, staring coldly at the man standing opposite her; even if John didn't want her to say anything that could incriminate her as a potential ally of his, she was not going to allow him to become the Atlantis scrapegoat. "If you possess a legitimate reason for attempting to find him, then you are, of course, completely within your rights to do so; I've never intended to imply otherwise. However, if you start making up excuses to go after him- such as accusing him of releasing this virus despite the complete lack of information that he's done anything like that-, I _will_ be forced to have you taken off active duty until I feel certain that you are not going to allow some… _personal vendetta _to affect your judgement."

"'_Personal vendetta_'?" Sumner repeated, glaring at her. "If you're-"

"I've already tried to make it clear that I understand your position on the Phantom; it's only when you start accusing him of committing crimes without evidence that I will actively attempt to oppose you," Elizabeth said, her tone cool as she continued to glare at Colonel Sumner. "As I told you yesterday, you are _not _going to turn this hunt for the Phantom into the Salem Witch Trials; I respect that his status as an independent operative in the city might put us at risk in a time of crisis, but I will _not _permit you to accuse him of doing something when you have no evidence. When you have genuine evidence that he has committed a crime, then you can feel free to present it to me; otherwise, the Phantom is innocent of any possible malicious intent until you can prove that he is guilty. Understood?"

Further conversation was cut off when Doctors McKay and Beckett walked into the office door, looking uncertainly between the two commanders as they glared at each other, Elizabeth silently daring Sumner to contradict her while Sumner looked back with an expression that made it clear he wanted to say something in defence of his earlier accusation despite a lack of inspiration for what that could be.

"You guys have a minute?" McKay asked, looking uncomfortably at Sumner and Elizabeth as the two of them turned to look at him and Beckett ; evidently the Canadian knew that he'd just walked into an argument but at the same time had no real idea what the conflict had been about. "We've been able to spend some, uh, quality time with the, uh, nanovirus samples."

"From what we can tell, they've all been incapacitated," Beckett added. "Looks like the Phantom was right about the wee buggers; the computers that ran them were shut down by the EMP pulse generated by the detonation of the naquadah generator, but the pulse was too far away to affect any of our technology while it was in its dormant state."

"Well, that's good to know," Elizabeth said, nodding at Beckett with a slight smile; at least she knew that the Phantom had told them the truth about that (Maybe it would help her convince Sumner to go easier on the Phantom in the future; he'd had the chance to potentially cripple their ability to run the city by shutting down their own technology while leaving his own ability to control the city unaffected, and yet he'd gone out of his way to let them know what he was planning so that wouldn't happen).

"Yes," McKay confirmed, nodding briefly at her before his face became more solemn. "Also, upon further investigation, I think we can rule out that they were created by the Wraith. Putting aside the fact that the Wraith wouldn't have any need for a WMD- they're killing us because they need us for food, not because they sadistically want us dead-, they're different than any Wraith technology we've come across thus far."

"If not the Wraith, then who made them?" Sumner asked, looking critically at the Canadian scientist.

"Well," McKay said, as he looked over at the colonel, "so far we haven't discovered anything to contradict the Phantom's claim that they were an Ancient weapon that didn't quite work out the way they'd planned; they certainly _look _like they could have elements of Ancient technology involved in their construction, but there's really no way to be _sure _unless we can find something else about where the Ancients acquired the virus in the Ancient database…"

"Work on it as soon as possible," Sumner said, looking pointedly at McKay before he turned back to look at Elizabeth. "I'll be issuing orders to increase the security patrol rate as soon as we're certain all strands of the virus have been eliminated from Atlantis."

Elizabeth opened her mouth to try and object- how often did she have to repeat herself before Sumner understood that she wouldn't accept him automatically treating the Phantom as though he'd already proved he had malicious intentions towards the city?-, but Sumner cut her off before she could even say the first word.

"This is _not _about the potential danger he could pose," he said, looking pointedly at her to make it clear that he'd taken what she'd said earlier into account. "This is in response to the fact that he clearly knows more about the city than we could have expected, after an experience like this, I think it proves that we could use his knowledge in getting a better idea about how this city operates."

"And what if he has his reasons for wantin' to stay independent?" Beckett asked, looking over at Sumner with a critical expression. "For all you know he might have valid reasons for not wantin' to let us know about what's in some parts of the city-?"

"If he has valid reasons for not telling up about himself, I'll accept them when I hear them; until then I have to proceed on the basis that he's a potential threat," Sumner replied, looking pointedly at the doctor before he turned back to face Elizabeth. "I'll send you reports on the new security team layout as soon as I have it arranged, Doctor Weir; in the meantime, make sure that your people know the situation."

With that, the colonel turned around and walked out of the office, leaving the three doctors alone as they looked at each other before McKay broke the silence.

" 'Your people'?" the Canadian repeated once Sumner was out of earshot, shooting a glare after Sumner that suggested he would have hit the commander if he'd been present. "What, does that include _everyone _who isn't part of his 'military chain of command' thing?"

"Well," Elizabeth said, trying to phrase her response in a manner that wouldn't reveal her true feelings about Sumner's orders to McKay and Beckett- as much as she trusted them, Sumner had made a valid point when he said that they needed to create the impression of a united front if they were going to cope in Atlantis; even giving these two the impression that there was dissent among the city's two leaders could cause problems-, "it's all a matter of prioritising, really. Since the military members of the expedition tend to view Colonel Sumner as _their _commander, I'm generally seen as the leader of the civilian population, so he probably considers it only sensible that I be the one to make sure you and your respective staff members know about his plans regarding the Phantom…"

"Yeah, talking of the Phantom, what is Colonel Sumner's _problem _with the guy?" McKay asked, looking over in frustration at Elizabeth. "I mean, I'm not saying that masked guy was _right_ in not telling us that the Ancients had created a virus that would have killed almost a third of our population if it got out- and I'm still not entirely happy about him shooting me like he did-, but this whole 'we must eliminate the Phantom' thing the Colonel's got going on is just _ridiculous_!"

"I have to agree with Rodney, Elizabeth," Beckett added, looking over at her with a slightly grim expression. "The Phantom might not have told us much about himself, but everything he's done so far has definitely helped us out of situations that we might not have been able to handle ourselves; how can Sumner _still _say he's a threat when the man hasn't done anything more serious than stun us when he doesn't have the time to talk?"

"It's… just the colonel's nature; he doesn't like having an unknown element introduced into the city in a situation like this," Elizabeth said, constantly reminding herself that she wouldn't help John in the slightest by speaking out too vocally in favour of him and attracting attention to herself for her attempts to speak out in his defence. "He's a military man by nature; as far as he's concerned he needs to know everything about the situation we're in if he's going to properly defend us-"

"Yeah, _defend _us when he's barely even made a real effort to get to _know _us beyond our essential skills!" McKay groaned, staring briefly upwards in frustration. "Don't get me wrong, he's a good team leader when we're out in the field, but seriously, have you ever seen him even bother to spend time with us _outside _of missions?"

"He did arrange for you and Teyla to receive training-" Elizabeth began.

"Oh yeah, learning how to kill people; that's a _really _great bonding activity, isn't it?" McKay countered as he glared out of the door in the direction that Sumner had just walked. "I mean, at least Ford actually _tries _to socialise with me and Teyla now and again; every time I try and talk with Sumner when we're off-duty about something that isn't related to the next mission it's like trying to get blood from a stone! I get that we're in a military situation and we have to exercise 'professional detachment' in case our personal feelings cloud our judgement when we're in action, but come _on_, would it be asking that much for him to show more interest in us as something other than his _job_?"

"Colonel Sumner has his way of doing things; as long as he's the military commander, we need to accept that," Elizabeth said, wishing that she could tell McKay she agreed with his opinion without actually going against John's wishes (And why was his opinion so _important _to her?). "I assure you, I'm doing everything I can to prevent him from taking his… vendetta… against the Phantom too far, but otherwise there's really nothing I can do about his attitude towards his responsibilities on Atlantis. If he wants to maintain a professional detachment, that's completely his decision; I can hardly _order _him to spend personal time with the rest of you."

"_Fine_," McKay groaned, as he turned around and walked out of the room, shaking his head in frustration as Beckett and Elizabeth looked after him.

After a moment's silence, Beckett sighed as he walked over to sit down opposite Elizabeth.

"It's not exactly been easy, has it?" he said reflectively.

"Working with Colonel Sumner?" Elizabeth asked, looking over at the doctor with a slight smile. "I know he's not the… _easiest _person to get along with, and his methods can be a bit… harsh at times, but-"

"That's not what I meant, lass," Carson said- with only the two of them here now Elizabeth felt more comfortable thinking of him by his first name-, looking at her with a slight smile. "I meant having to let the colonel go after the Phantom."

Elizabeth blinked.

"W-why would that be… difficult?" she asked, wishing she didn't sound so surprised; it hardly helped the impression that she had no personal interest in John's safety. "I've told you, I see Colonel Sumner's reasoning-"

"Elizabeth, you and I spent a lot of time together down in Antarctica while we were sorting out who we wanted for this expedition, and I think I got to know well enough to know when there's something you're not telling people," Carson said, a slight smile on his face as he looked at her. "I saw you when you were talking about how you and the Phantom dealt with that shield issue we had during the storm; you spent a _bit _more time with him than you're telling us, aren't you?"

For a moment, Elizabeth could only stare back at Carson as the Scottish doctor smiled at her, before she finally sighed in resignation.

"Well… maybe a _little_," she said at last, trying to think of a way of phrase what she was about to say without actually giving away how much she'd learnt about John during that brief meeting. "It wasn't much; he just told me that he had a safe way of getting around the city that would allow him to avoid the lightning strikes, told me that he'd spent a great deal of time learning how to operate Ancient technology, things like that…"

"You mean you really _did _speak to-" Carson began, before Elizabeth held up a hand.

"Please… don't ask me anything else," she said, looking earnestly at Carson. "It's not that I don't _trust _you; it's… well, it's…"

"Complicated?" Carson asked, another slight smile on his face as he looked at her, only a faint trace of disappointment in his eyes. "I understand; you'd… rather some things stayed private, right?"

"It's not that they're _embarrassing_ or anything like that," Elizabeth said as Carson moved to stand up, not wanting her friend to get the wrong idea about her motives. "It's just that…"

She sighed. "As Rodney said, the Phantom hasn't actually done any _harm_; I just… don't feel like there's any point in talking about it when it doesn't really have any bearing on anything."

For a moment Carson simply looked at her in a manner that suggested to Elizabeth that he knew she wasn't being totally honest with him- he'd always been able to read her rather well in that manner; she had never been sure if his ability to know how much people were telling him was part of his medical training or part of his own personality-, but he finally nodded in understanding and stood up.

"Fair enough," he said, as he smiled slightly at her. "Just remember, if you need someone to talk to about all this, my door's always open."

"Of course," Elizabeth replied, nodding back at Carson as he walked out, leaving her sitting alone in her office once again, the paperwork still spread out before her.

_Well_, she mused to herself, glancing around her office, _that went as well as could be expected_.

On the one hand, it was nice to know that she wasn't the _only _one who thought that Sumner's attitude towards the Phantom was exaggerated, but she still didn't really know how anyone would react to the idea of her actually… _feeling _something for him beyond simple curiosity.

Hell, _she _didn't even know how to feel about it; she wasn't even sure _what _she was feeling! She'd barely even spoken to the Phantom beyond what was necessary to convey the immediate information about whatever crisis they were currently up against, she knew nothing about him as a person beyond his first name and the fact that he'd been active in the Pegasus Galaxy for the last decade or more-

Elizabeth paused.

_Hold on a minute_… she thought, almost ashamed that she hadn't realised it before. _'John' isn't a name native to this galaxy… so how did he get it_?

It was always possible that the Phantom had told her a false name, of course, but Elizabeth didn't entirely believe it; his hesitation might have suggested he was thinking up something aside from the truth, but even with the cloak concealing most of his body from view, Elizabeth knew enough about body language to feel confident that he'd told her the truth about his name.

If anything, that only added to the mystery that seemed to be growing about the Phantom. While the idea that he came from Earth would certainly account for him installing that program that prevented them from dialling Earth- he'd worked out Earth's address and hadn't wanted the Wraith to be able to access the planet if they found Atlantis-, it did nothing to account for how he was meant to have come to the city in the first place.

Even if he'd come here by means other than the Stargate, once he'd discovered Earth's address, why hadn't he simply used the Stargate to go back? After all, it was only the Stargate that _dialled _the wormhole that needed to have power; according to McKay, the receiving wormhole could take over if there wasn't enough power at the point of origin to maintain the wormhole long enough for someone to travel through it, but otherwise power was only required at the sending end. The Stargate Program may not have existed at that point, but the Stargate itself had already been transferred into the Cheyenne Mountain Complex for testing; it would have been a shock when it dialled, but the Phantom could surely have dialled Earth without any trouble…

_Great_… Elizabeth groaned, as she slumped back into her chair, one hand pressed against her forehead. _Even the _answers _I get only leave me with more questions_…

She acknowledged that John- or whatever his full name was- must have his reasons for not telling her everything, and she'd respect them unless the time came where she felt that she was in a position where she _had _to learn the answers…

That didn't mean she couldn't feel frustrated at the mysteries his presence was presenting to her, did it?

* * *

Even as Elizabeth pondered the mysteries of the Phantom's existence, the subject of her thoughts was currently crouched above her office, silently watching her as she spoke to her senior staff, conflicted thoughts flying through his head.

On the one hand, he was grateful for this new evidence that Elizabeth wasn't alone in not regarding him as the threat that Sumner perceived him as; his brief conversations with Teyla and Doctor Beckett notwithstanding, talking to people when you were your only hope in a crisis situation didn't guarantee they'd accept you when the situation was calmer. As it was, however, their brief conversation just now had made it clear that McKay and Beckett at least sympathised with him and acknowledged that he might have his reasons for his actions, even if McKay clearly wasn't as big a 'fan' of his as the other two.

On the other hand… the casual way in which Elizabeth and Doctor Beckett had spoken to each other… the way that he'd called her 'lass' in that accent of his… the way the doctor had looked slightly disappointed that she wasn't telling him more about her meetings with him… his casual comment about how they'd spent a lot of time together back on Earth…

He'd sworn long ago that he'd never attack anyone unless they gave him a reason to do it, but right now he was strongly tempted to take his gun and see about rearranging Beckett's-

_NO_! he berated himself, cursing as he turned around and began to crawl along the maintenance tunnel to his current hiding location (It was about time for him to see about having a meal anyway; _anything _to distract him from his current line of thought).

As he'd reminded himself only a short time ago, _nothing _mattered but that Elizabeth was safe.

If it meant that she was safe to live her life with some doctor with a stupid Scottish accent who couldn't even be bothered to shave properly- it seemed like every time he saw the guy he had at least a day's worth of stubble; it made him look like he couldn't decide whether or not to grow it out-, he'd just have to deal with that.

Her safety was the _only _thing that mattered.

He had protected Atlantis so that she would have a chance to live a proper life in it; if that life was with him, he would have… liked it, of course… but if it wasn't, he would settle for what made her happy.

If only it didn't _hurt _so damn much…

_God_… he groaned, as he felt the faint trace of his tears begin to gather around the eyeholes of his mask. _Just _once_… I'd like something to work out _my _way…_

He knew it was selfish, but he couldn't help it; ever since he came to this city, she'd been the only good thing that had ever really happened to him…

Hell, she'd been the only good thing in his life, _period_; she had made him feel like he was worth something when his own _family _didn't seem to care what he wanted to do, making him feel like crap every time he objected to his father's-

_STOP IT_! he cursed himself. _NO living in the past, remember_?

His life now might not be perfect, but he was doing what _he _wanted; that was more than most people ever managed to have the chance to accomplish.

If only he could stop himself from wishing that he could have that one last thing for himself, everything would be fine…

_God, I _really _hate Scottish accents_.


	21. The Power of the 'Dream'

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: OK, now these _next _few chapters are going to be interesting ones- at least, I hope they'll be interesting ones-, given that they take a more direct look at how the offowrld team handle a mission with _Sumner _in charge as opposed to _Sheppard_… specifically, looking at Chaya's 'return' to Atlantis (To say nothing of how John would interact with her in _this _timeline)

The Phantom of Atlantis

As the gateship left the Stargate to swiftly enter into orbit around the next planet on their list from the Ancient database- it was _definitely _a relief to be able to just enter the addresses as they were; apparently the database in the city was programmed to automatically update the Stargate addresses to compensate for any stellar drift that might have occurred since they were originally created- Colonel Sumner allowed himself a slight smile as he glanced over at where Doctor McKay was sitting in the pilot seat.

The Canadian scientist had requested the opportunity to fly the jumper on this occasion rather than Sergeant Markham- his official reasons being that he wanted to 'practise with the Ancient gene' when anyone could see he just wanted to fly the thing-, and Sumner had quickly agreed. He might try to encourage professionalism from his team, but he was simultaneously willing to allow them the opportunity to explore new talents; he had little real interest in flying himself, beyond its ability to rapidly get him from one point to another, but at the same time he couldn't deny its importance in the daily activity that they had to endure since they had arrived in the Pegasus Galaxy. Sergeant Markham was a decent pilot, but given the advantages of the simplicity of the traditional four-man-team structure that had been organised back on Earth, he preferred not relying on the sergeant's abilities unless he had to; adding an extra man for even a short-term basis tended to throw off the team dynamic.

With a relatively relaxed mission like this- just scouting out a planet to see if there was anything interesting on it-, he'd considered it the perfect opportunity for the scientist- the most aeronautically-minded amongst them; he and Ford weren't pilots by training and Teyla's people had barely even mastered the wheel, while McKay had at least been involved in the development of some details of the plans for the _Prometheus _and the F-302s- to get in some practise at flying the gateships. He would never have the natural feel for it that some members of the expedition had displayed, but he could do a fairly good job when he was in the control seat; in this kind of situation, it was the perfect opportunity to give McKay some much-needed practise.

"Anything interesting?" he asked, glancing over in McKay's direction after a couple of minutes had passed since exiting the Stargate; normally he allowed his team to wait and report anything they discovered, but there always came a time when the need for answers took priority. A couple of seconds after the words were out of his mouth, the HUD appeared on the screen before them, displaying the relevant information as McKay's subconscious mind processed the question and 'told' the gateship what they wanted to know. It was never quite as quick as Sumner would have liked, of course, but even the members of the expedition with the strongest Ancient gene couldn't make these systems operate faster than McKay was capable of at the moment.

"Scanners don't show much in the way of habitation; looks like only a few small villages centred around one location," McKay said, shaking his head as he glanced back over at Sumner. "I'll take a quick orbit around the planet just to make sure, but I'm pretty sure if there _was _anything interesting enough to attract our attention we'd see it already…"

"No harm in making sure," Sumner said simply as he sat back in his seat as McKay took the gateship into orbit. As much as he hated to admit it, none of the expedition had a natural 'knack' for Ancient technology to the extent that they received an instantaneous reaction; it always seemed to take them an admittedly slight but nevertheless noticeable amount of concentration in order to trigger a response from the machinery in question.

It was one reason the Phantom's continued existence worried him so much; from what they'd seen of the man's ability to control Ancient technology so far, there was a very good chance that he could easily override anything they wanted Atlantis to do if he wanted.

Hell, from what he'd overheard during the Genii invasion, the man was already immune to Atlantis's internal sensors; even if he _did _discover evidence that the Phantom was a legitimate threat and was able to convince Doctor Weir to arrange a larger-scale search, how could he track someone he couldn't even-

The gateship suddenly shuddering as though it had hit sometime distracted Sumner from his thoughts about the Atlantis situation; the sight of what looked to him like Wraith weapons fire passing alongside them only confirmed his fears.

"Wraith darts?" he asked, glancing over at McKay.

"Unfortunately, yes; looks like two of them," McKay replied, his tone brief for once as he moved the gateship in what only the view through the viewscreen told Sumner was a spin; he might not always understand how the inertial dampners worked, but there were definitely times when they were a distinct advantage.

"If my opinion matters to anyone, I recommend shooting back any time now," Ford added, looking

"I'm sorry, do you think I haven't _tried _that?" McKay countered, turning to glare at Ford. "The hit must have caused some damage, and right now I _don't _think this is the time to conduct repairs!"

"Where did they _come _from?" Teyla asked, looking out at the viewscreen questioningly.

"Excuse me?" Sumner asked, looking back at the Athosian in confusion.

"These ships are only short-range fighters," Teyla pointed out (There were definitely times when Sumner wished he'd spent more time at the SGC; he just wasn't _used _to thinking of facing opponents like this). "If they did not come through the Stargate- which, based on the direction they came in, they most likely did not-, a hive ship must be close by-"

"In which case we need to get out of here fast," Sumner concluded, quickly turning to look impatiently at the pilot while also making a mental note to spend more time thinking about possible threats he might face in this job; he'd been so focused on figuring out how to cope with the Phantom that he'd almost forgotten that the man wasn't the only threat he had to deal with. "_McKay_!"

"I'm working on it; it's not like we're on the same side of the _planet _as the gate right now!" McKay countered, glaring over at Sumner in frustration as he tried to keep the gateship moving in a manner that would prevent the Darts locking on to them without giving them the opportunity for a lucky shot.

"Couldn't we lose them in the atmosphere?" Ford asked, looking over uncertainly at the Canadian.

"Worth a shot," McKay replied briefly. "Just give me a few…"

His voice trailed off as he stared at the HUD currently displayed before them. Sumner might not have been certain he knew what every symbol on the device said, but he was fairly sure that the massive cloud of something that currently seemed to be coming out of the planet below them wasn't a normal occurrence. Almost as soon as they'd registered its presence, it swept over the small dots on the HUD that demonstrated the current location of the Wraith darts before it continued to envelop the gateship.

"Hang on!" Sumner yelled, as the cloud- which seemed to be formed completely out of brilliant blue lightning- surrounded the gateship, crackling around the edge of the viewscreen before it suddenly faded away as quickly as it had appeared, leaving the four-man team staring incredulously out at the empty space that now surrounded them once again.

"The Wraith darts have been destroyed," Teyla said after a moment's pause, staring in awe out of the viewscreen at where the 'storm' had so recently surrounded them.

"Well… Ford muttered, staring in surprise at the suddenly empty space behind them, "at least that's _something_."

"I…" McKay gasped, turning around to look incredulously at the rest of the team. "I… I thought we were _dead_… Anyone else think we were dead?"

"What the hell _was _that?" Ford asked, indicating the screen that had so recently displayed the storm.

"Some sort of energy weapon, most likely…" McKay muttered, evidently unwilling to commit himself until they knew more either way.

"Quite…" Sumner reflected, nodding thoughtfully before he looked back at them. "Shall we take a look?"

"Definitely," Ford confirmed, nodding back at the colonel. "Something that effective, we _definitely _need to find out more about it."

"Personally speaking, right now I'm just grateful not to be dead, but I'm all for finding out why," McKay added, as he turned the gateship around and set it on a course towards the planet. "It looks like that… whatever it was… came from near the village I detected earlier; I'll take the ship down there and see what we can find."

"Any theories?" Sumner said as he looked quizzically over at his team scientist.

"Well, aside from the fact that it's an energy weapon that somehow destroys darts while leaving us without even any electromagnetic pulse-related damage, I think we can safely conclude that…" McKay began, before he trailed off and shrugged apologetically. "Nothing. I have nothing to conclude; I'm just… talking for the sake of talking."

"Ah," Sumner said simply, deciding to leave it at that; after so long hearing McKay go on about he was an expert in pretty much everything to do with Atlantis, it was a pleasant change to encounter something that made him be quiet.

"Could something like that be… naturally occurring?" Teyla asked, breaking the silence that had settled over the cockpit as it continued towards the planet.

"I doubt it," Sumner said simply. "Most likely it's a weapon the Ancients left behind."

"_Of course_…" McKay said, shaking his head in what Sumenr was fairly certain was a self-criticising manner- not that he got the opportunity to see it often; the problem with working with somebody as smart as McKay was that he tried not to let you know when he didn't think of something- as he looked eagerly over at his teammates. "And any weapon that powerful would have to be powered by…"

"A Zero Point Module?" Sumner concluded.

"Correct," McKay said, nodding resolutely at his commander. "We are _definitely _going down there."

Sumner wasn't going to deny the accuracy of McKay's statement; even if they weren't going to _take _the ZPM from the planet- Doctor Weir had been angry enough when they'd taken the ZPM from M7G-677-, it was always possible that the weapon might have a couple of back-up power sources nearby that they could use. Their current ZPM would do them for a while, of course, but its limited amount of power meant that they were still reluctant to rely on it to charge up the entire city; even with their naquadah generators covering more of the basic essentials, there was so little power left in the ZPM that they were reluctant to use it unless they had to…

* * *

A couple of hours later, the four of them were crouched in the trees on the other side of a river, studying the primitive- Middle-Ages-style dwelling on the opposite side of the river where the gateship had landed; Sumner had concluded that there was no sense causing a panic by arriving via ship.

"If there's a weapon down here, sir," Ford commented, the young lieutenant looking at the village before them through his binoculars, "these folks didn't build it."

Sumner had to agree with that assessment; even allowing for the possibility that the species here had opted for a 'back to basics' approach, he strongly doubted that they'd have gone so far 'back' that they didn't seem to even have anything more than basic technology available.

"More evidence for the 'lost Ancient weapon' theory at least," he mused, before he glanced over at where McKay was impatiently studying an Ancient scanner. "Picking up anything?"

"I'm picking up everything," the Canadian replied in a sullen tone. "Just nothing worth mentioning."

"Well then," Sumner mused- given the orbital nature of the current Stargate, there was no point asking if Teyla's people had been here in the past-, "time to take a closer look."

With that said, he and the team began to slowly approach the village, Sumner taking care to ensure that their weapons were available without giving a potentially negative impression of combat-readiness, until they finally reached the village. As they walked further into the village, Sumner noted the almost stereotypically Indian-like costumes of the villagers, each of them possessing elaborate tattoos. The only person who seemed to be wearing more practical clothing was a bald man in red robes, who ran off towards a house off in one corner of the village when he saw them approaching, leaving them to look silently at the gathered villagers.

"Uh… hello," Sumner said, nodding slightly at the villagers around them as the team advanced into the village, uncertain what else to say in this situation; he was _never _entirely comfortable in first contact situations like this, and the fact that they had an orbital gate only made the situation worse. "It's OK; we're… we're not here to cause trouble."

"It is likely they have never seen anyone from outside their village," Teyla said, briefly stepping forward to address Sumner in a low voice; once again she demonstrated the diplomatic attitude that had prompted him to recruit her for his team in the first place.

"Welcome," an old man in a red robe said, breaking the silence that had apparently settled over the villagers as he walked through a small bridge off to one side, followed by a group of men in identically-coloured robes. "I am Zarah, one of the abbots of Proculus."

"Colonel Marshall Sumner," Sumner said, nodding briefly in response to the man's introduction; so far this guy's robes were the most complete clothing he'd seen, which at least suggested that he was one of the people in charge here. "This is Teyla Emmaggan, Lieutenant Ford and Doctor McKay."

"Please, come," Zarah said, nodding briefly at the group before he turned around, heading towards what Sumner could only think of as a hut without any walls- he couldn't help but look slightly uncomfortably at it; these people had _no _sense of security or privacy-, just off to the side of the bridge that he and his fellows had entered by, a low table in the centre of the building suggesting that it was a communal dining area of some kind.

"This is the first time- at least in my own lifetime- that people from another land have come to us," Zarah continued as the team sat down around the table. Sumner wasn't certain if he should take the broad grin on the man's face as a good sign or something that he should be concerned about; it was almost… _too _enthusiastic, in his opinion.

"We came by ship," he said by way of explanation, concluding that he might as well start testing the level of local knowledge with the basic essentials (Plus, of course, asking about that weapon they'd seen in action straight away would probably create the wrong impression; they didn't want to appear _too _military-focused too early).

The uncertain expression Zarah assumed at his words was all Sumner needed to confirm his initial assessment from the first look at the planet's civilisation; these people definitely _weren't _very technically advanced.

"A machine that flies through the sky," he continued; the confusion could have simply been because the man assumed he was talking about a boat despite the lack of a decent-sized river fanywhere near the village. "It allows us to move from one world to another."

"Another world?" Zarah repeated, looking in confusion at Sumner, clearly not understanding the explanation.

Sumner only just managed to stop himself from groaning in frustration. It was beginning to look increasingly likely that McKay's 'abandoned Ancient weapon' theory was accurate, although the weapon in question was almost certainly automated, given how low-tech these people seemed to be from what Sumner had seen of them so far.

"From among the stars you see in the night sky," Teyla put in, picking up the explanation. "We are peaceful explorers."

"Well then," Zarah said, evidently satisfied with that explanation for the moment despite his evident confusion, "glory to Athar for bringing you here safely."

"Athar?" Ford repeated, looking inquiringly at the man.

"The provider… and protector of all," Zarah said, looking over at Ford with a tone in his voice that suggested to Sumner that the other man was wondering if the young lieutenant was stupid. "Surely you know?"

"Athar is known by many names among the stars," Teyla said before Ford could speak himself, apparently satisfying Zarah's curiosity. Sumner had to admit, he liked the way the Athosian had phrased her response; acknowledging these peoples' beliefs without confirming or denying that they shared it, while also leaving room open for interpretation in case 'Athar' was an Ancient who had once lived on this planet and provided them with that weapon they'd encountered rather than merely a more metaphorical god.

"Is… uh… Athar around?" McKay asked, looking over at Zarah in a manner that Sumner had come to recognise from past experience; it was McKay's expression when he tried to give the impression that he knew what he was talking about. "We'd love to talk to him. We're…friends."

Sumner had to fight to stop himself from rolling his eyes in frustration at McKay's ineptitude; there were _definitely _times when his team couldn't understand the need for silence on some occasions.

It was just as the Canadian had said when Commander Kolya was attempting to force the two of them and Doctor Weir to repair the last grounding station during the storm a few weeks ago; the man couldn't bluff to save his life, even about the little things like whether or not they 'knew' this planet's 'god'.

"Athar is friend to all," Zarah replied, his tone once again suggesting to Sumner that he and his people took this as a fact (The colonel was just grateful he hadn't denounced McKay as a liar; this meeting looked like it would be awkward enough without those issues to take into account). "And with us always… Even now," he continued, placing his hands together in a gesture that Sumner assumed represented prayer; the military part of him wondered if the clenched hands represented a willingness or ability to do violence, or had some other lost meaning that he was missing.

"Of course," McKay muttered, raising his hands slightly as he glanced up at the ceiling. "_Hi_, Athar."

"What Doctor McKay means is that we wish to offer our thanks," Teyla put in, smiling reassuringly at Zarah; she might lack the formal military training of the soldiers Sumner had selected on Earth, but her diplomatic abilities were definitely not to be questioned at times like this. "We were attacked by the Wraith and would have been killed had it not been for Athar's intervention."

"Wraith?" Zarah asked, looking at Teyla in a manner that made it clear to Sumner the man had no idea what Teyla was talking about.

The colonel blinked in surprise.

_This _was new…

_A civilisation in this galaxy that_ doesn't _know about the Wraith_? Sumner reflected. _This _definitely _merits further investigation… _

"You've _never_ encountered the Wraith?" he asked, looking quizzically at the older man as he tried to determine whether or not he was being honest. "Tall, pale-skinned men, lizard-like eyes, typically dressed in black armour coats, they either make you vanish by scooping you up with their ships or they come down and drain your life out of you with their hands…?"

"We have never encountered such beings," Zarah replied, his evident confusion at Sumner's description too clear to be faked (Sumner wouldn't deny that his people skills needed work, but he _did _know when someone was lying to him).

"Never?" Ford repeated, his own curiosity matching Sumner's own.

"And there is no mention of them in your history?" Teyla asked; Sumner was only slightly relieved to note that this latest turn of events was just as surprising for Teyla as it was for him.

"None," Zarah replied, looking around the team as he was trying to decide whether he should take them seriously or not. "I can assure you that for many thousands of years we have lived here in peace."

A quick glance at the other members of the team was all Sumner needed to make up his mind; they _definitely _needed to talk about this latest turn of events in private.

"Could you… excuse us for a moment?" Sumner asked, as he looked uncertainly at Zarah; he had no way of knowing how the other man would react to them asking for privacy so soon after arrival, but the implications of this latest discovery were something that he and his team should definitely talk about by themselves.

"Of course," Zarah said, rising to his feet as he held out his hands in a 'stay' gesture. "Please, I must tell the other abbots of your arrival before we go to meet with Chaya."

"And 'Chaya' is…?" Sumner asked, looking quizzically at Zarah; regardless of the etiquette on this planet, he wanted to talk to someone in authority as soon as he and his team had a chance to discuss their recent discoveries about this civilisation, without wasting time on intermediaries.

"The high priestess of Athar," Zarah replied, before he placed his hands together once again and briefly raised them to his lips (Sumner wished the man would stop doing that; he'd been in the military too long to feel comfortable with somebody making fists in his presence). "This is a great day for our people."

"Uh… thank you," Sumner called after Zarah as the man left- at least it sounded like they'd be talking to someone important soon; given these peoples' evident dedication to 'Athar', the High Prestess would most likely be fairly important in a society such as this one-, quickly leaning in to the centre of the table as soon as the man had left the hut. "Can you _believe_ the potential applications of this?"

"I can scarcely comprehend it myself, Colonel," Teyla replied, her own broad smile reflecting the enthusiasm that Sumner himself was trying to keep in check; he had at least some kind of authority to maintain in this situation, after all. "Every inhabited world I have encountered in this galaxy has been ravaged by the Wraith, yet this one appears untouched."

"Well," McKay added, looking thoughtfully around at the others as he spoke, "that would certainly be the result of the Ancient weapon that saved our asses up there; it only makes sense."

"You sure about the Ancient thing?" Ford said, looking critically at the Canadian scientist.

"Well, there's no other explanation," McKay replied, his enthusiasm growing as he studied the group around him, as though trying to make sure they'd understood the implications of his current theory. "I mean the power requirements of something like that must be… well, 'astronomical' is putting it mildly; they'd _definitely _need a ZedPM to get it working…"

"And yet," Teyla added, uncertainty now on her face as she voiced Sumner's own concern, "they do not _appear_ to be technologically advanced…"

"We should consider the possibility that Zarah's lying," Ford pointed out, looking over at Sumner as though seeking acknowledgement of his theory.

"True, but unlikely; he didn't strike me as the lying type…" Sumner said, nodding thoughtfully while trying not to explicitly dismiss the lieutenant's theory as he glanced over at McKay. "What do you think; automated defence system?"

"Assuming these people are telling the truth-" McKay began.

"We don't have any _evidence _that they're not; we shouldn't start jumping to conclusions," Sumner interjected, raising his hand to halt McKay's speech, Elizabeth's reprimand for his near-accusation of the Phantom with little to no evidence to back up his claim still ringing in his ears; regardless of his own suspicions, he wasn't going to _voice _any concerns he might have about this situation until he had evidence to support him feeling one way or the other.

"Well… in that case, until we learn anything else, 'automated Ancient weapon' seems like our best explanation for this planet's situation, yes," McKay confirmed, nodding at his commander

"Imagine a world where displaced refugees from… _dozens_ of planets could come and live in _peace_, without fear of being culled by the Wraith," Teyla added, the broad smile once again returning to her face as she looked around at the others.

As much as he preferred to consider the potential military applications this place had to offer- a guaranteed Alpha Site was something the expedition could certainly use, as far as Sumner was concerned-, he had to admit that Teyla made a good point; if this planet's people would agree to permit their world to become a refugee camp for others, they could simultaneously save innocent lives _and _deprive the Wraith of a significant portion of their food supply.

"Maybe we could negotiate some kind of treaty," Ford added, looking uncertainly between Sumner and Teyla; Ford was a good soldier, but Sumner sometimes worried about his need for validation from his superiors.

"We just need to get access to that weapon and see what we can learn about it," McKay cut in. "Better still, we can find that ZedPM- _not_ that we'd steal it or anything," he added, as Sumner turned to look pointedly at him; Elizabeth had nearly had the entire team's heads after they'd come so close to unintentionally dooming that planet to attack while examining their ZPM, Elizabeth had made it clear that modules were only to be taken back to Atlantis when it was certain they were fulfilling no function at their current location.

"For now," the colonel said, as he turned to look at Teyla and Ford- he didn't like 'singling out' any one member of his team; it didn't exactly encourage an easy working environment if he gave the impression he didn't trust or like one person in particular-, "everyone simply remain natural and avoid causing offence; if we're going to reach any kind of agreement with these people, we need to tread carefully."

"Of _course_," McKay said, the Canadian almost sounding offended at the implication that he would be anything other than polite.

Sumner didn't bother replying to that comment; right now, the sooner they went to meet with this 'Chaya' person and established some kind of framework on which to begin their attempts to negotiate an arrangement of some sort, the happier he'd be.


	22. Chaya Sar

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: I apologise in advance for the absence of the Phantom in this chapter; I _assure _you that he returns in the next one

The Phantom of Atlantis

The subsequent walk to Chaya's home- nobody had specified whether it was a house, a temple, or something in between, and Sumner hadn't wanted to ask in case it gave the wrong impression about them- was relatively uneventful, even if McKay's constant complaining about the distance swiftly wore on Sumner's nerves. He was just grateful that the priests didn't seem that bothered about the Canadian's complaints; the man might be one of the more talented people with the Ancient gene- even if he'd only acquired it via the gene therapy- but Sumner nevertheless wasn't ashamed to admit that he often wished the man would stay quiet sometimes.

Eventually, after they'd walked for such a distance that Sumner was starting to lose track of time- watches weren't that relevant anyway given the different solar cycles of most of the worlds they'd encountered after travelling through the Stargate-, they arrived at what Sumner assumed was their destination; a large stone building, presumably the remaining ruins of a temple of some kind, filled with various assorted plants, both in pots and in borders around the temple. A few Indian-style masks and tapestries were also visible from outside, clearly displayed on the pillars and walls that remained standing inside the temple, with only a thin wooden gate serving as any kind of actual 'barrier' into the temple; the plants around the walls gave Sumner the impression of having been grown for the visual effect rather than out of a desire for protection.

As the four of them- along with the three priests who had escorted them to the building- entered the gate, they were soon greeted by a woman who even Sumner had to admit was strikingly attractive, with honey-coloured hair and tanned skin, dressed in a light blue dress and a blue-beaded necklace with a white circle in the centre.

"Glory to Athar," Zarah said, bowing at the woman as she approached them, confirming Sumner's conclusion that the woman in question was the high priestess- Chaya, he recalled her name was- that Zarah had mentioned earlier.

"Welcome," Chaya replied, nodding slightly at him before she indicated a room off to one side. "You may rest."

"Thank you, sister," Zarah replied, he and the other monks subsequently departing to leave the team alone with the woman.

"You're new to Proculus," she said as she looked at Sumner, the comment clearly a statement of fact rather than a question.

"Correct," Sumner replied, nodding briefly back at her; it was always best to stick to the facts in this kind of situation until you had a better idea of where the situation stood. "Colonel Marshall Sumner."

"I am called Chaya Sar," the woman replied, confirming her identity as she briefly took his outstretched hand in both of hers- Sumner wished she wouldn't do that; that kind of gesture always made him feel like the people who did it were trying to stop him doing something- before turning to the others. "And you are…Teyla… Lieutenant Ford… and Doctor McKay."

"How did she know that?" Sumner heard Ford whisper behind him. He could only hope that Chaya couldn't see the lieutenant's no-doubt obvious discomfort at her knowledge; trust was a two-way street, and they weren't going to win Chaya's friendship if they gave the impression they didn't trust _her_, even if he never completely trusted anybody until he'd spent more time getting to know them (It had taken Teyla the better part of a month until he felt comfortable enough giving her a P-90).

"Oh please; one of the abbots ran ahead," McKay replied dismissively; once again, Sumner could only hope that Chaya hadn't actually managed to hear McKay' s casual dismissal of her knowledge.

"It is a pleasure to meet you, Chaya," Teyla replied, bowing her head slightly, thankfully providing an easy distraction from McKay's attitude.

"You must be tired after your long journey," Chaya continued, as she looked around at the others. "Shall I prepare some tea for us?"

"That would be… fine," Sumner said, nodding briefly in response. It wasn't exactly the perfect way to open negotiations- he'd prefer something more professional than sharing a drink, even if the drink apparently wasn't alcoholic-, but at least it put them on a more casual ground with which to open conversation.

As the group sat down around a small circle of seats towards the middle of the temple, the assorted abbots joining them as Chaya poured a strange-looking tea that Sumner couldn't immediately identify while Teyla explained the dangers presented to the worlds of the Pegasus Galaxy by the Wraith, citing the example of the culling that had driven her people from Athos and all the way to Atlantis for refuge.

"And where do they come from, these… Wraith?" Chaya asked as Teyla finished telling her about Athos's last culling.

"They seem to be everywhere in this galaxy," Sumner said, taking a brief sip of the tea- it was actually rather nice; he'd need to remember to ask for the plant they grew it from- before he continued. "They've caused a great deal of fear and terror on pretty much every planet we've visited for a significant amount of time."

"It's terrifying," Chaya replied solemnly; Sumner wasn't sure whether to approve of the apparent detachment in her tone of voice or feel frustrated at the lack of physical response he was receiving as he attempted to determine her real feelings about the matter. "Truly terrifying…"

After she had sat in silence for a moment, the woman turned and inclined her head slightly in Teyla's direction. "My heart goes out to your people, Teyla."

"It is not only my people who suffer, Chaya," Teyla replied, evidently concluding- as Sumner had- that the time to get to the point was now. "The Wraith have awakened from a long sleep, and this _entire_ world is safe from the culling that has already begun. Even Atlantis, with all its wonder, may not survive the onslaught. It is our hope that Athar could grant… sanctuary, here on Proculus."

"Sanctuary?" Chaya repeated, exchanging a brief, anxious glance with Zarah as he stood off to one side. "For so many?"

"Obviously we wouldn't expect you to provide a refuge for every other planet out there," Sumner added; there was no point overwhelming a valuable resource, after all. "However, you can hardly deny that your world is large enough to cope with any… guests who might arrive."

"More importantly," McKay added, "it's protected by that weapon of yours-"

"Weapon?" Chaya repeated, looking over at the Canadian in what even Sumner had to admit was evidently confusion. "I'm aware of no such thing on Proculus."

"Oh please…" McKay said, shaking his head slightly before he turned look directly at Chaya; given that Sumner wanted the woman to understand the scale of the situation just as much as McKay evidently did, he saw no reason to halt the scientist's speech unless McKay started to become too hostile or offensive towards her, so simply allowed him to continue speaking. "Chaya, the only reason we are alive is because of a powerful energy weapon that emanated somewhere on the surface of this planet. It destroyed the ships that were shooting at us; _that weapon_ is what's keeping the Wraith away."

"No, Doctor McKay," Chaya replied, her tone of voice suggesting that she was almost surprised that the alternative explanation she was about to suggest hadn't occurred to him. "It was Athar who protected you."

"Athar," McKay repeated, scepticism evident in his voice.

"Yes," Chaya replied; Sumner vaguely registered Zarah looking at McKay in what was probably the closest thing to a glare he'd seen anyone on this planet assume, but Chaya herself appeared to be perfectly calm about McKay's lack of belief in her religion. "Athar saw you were in need."

"And _that_ is what makes your world so remarkable," Teyla interjected; evidently, she had determined that McKay's line of argument wasn't going to make any progress in convincing Chaya to help them. "There are a great number of people who, like my own, are in need because of the Wraith; all we ask is that Athar grant them the protection that she was gracious enough to share with us, while we share what we can with you in exchange."

Once again, the Athosian woman had reaffirmed the reasons why Sumner kept her on his team; she might lack for formal military training on occasion, but she always knew when the time was right for her to step in and use her own skills where those of the others wouldn't do the job

"I understand," Chaya said, nodding . "I shall consult with her now."

Initially Sumner and the rest of his team stood up as Chaya and the monks did so, but Chaya quickly held out her hands and shook her head at them.

"Please stay here," she said, only a slightly apologetic look on her face to demonstrate her feelings on the matter. "I don't know how long this will take."

"Understood," Sumner said, nodding briefly at Chaya as she and the monks turned and walked out of the room.

He wasn't happy about it, of course- having potential allies leaving the negotiations to consult with their god wasn't something he was entirely comfortable with, particularly after everything he'd read in the SGC files about the Goa'uld-, but in the end he supposed he didn't have much of a choice if he was going to establish any kind of relationship with these people.

"'Athar grant them the protection that she was gracious enough to share with us'?" McKay repeated, looking incredulously over at Teyla. "Are you really buying this?"

"Questioning and doubting the religious beliefs of these people will not help us form an alliance with them, Rodney," Teyla replied, as she turned to look back at the scientist with a resolute expression. "It is always possible that, as you said, the weapon is a totally automated system that requires no action on the part of those here; could it not be that Chaya and these others are simply unaware of the weapon's existence as a weapon and instead believe it to be an artefact of some kind?"

Even as Sumner reflected that it was unlikely something powerful enough to destroy Wraith darts while they were in orbit could simultaneously be nothing more than some historical mystery to everyone _on _the planet- surely somebody would have noticed it in action by now?-, a part of him couldn't help but remember what Elizabeth had told him regarding his opinion of the Phantom back on Atlantis. He could never perceive the Phantom as anything other than a threat- the possibility that some day he would take some action or another that would hamper Atlantis's own ability to mount a defence due to them being unaware of it was too great-, but he would _not _attempt to 'frame' the Phantom for crimes he had not committed.

If he was going to obey that 'rule' on Atlantis, he was going to apply it to his duties on other worlds; he wouldn't start looking for potential threats or deceit when he had no evidence that any were present.

"We didn't imagine that weapon, Colonel!" McKay yelled, breaking into Sumner's train of thought. "We saw it with our own eyes-"

"And," Sumner interjected, glaring silently at McKay for a moment as he made certain the scientist understood who was in charge right now before he moved to sit back down, "until we know anything else about how this world operates, we should Let's just… wait and see what… Athar has to say."

"So… 'pay no attention to the man behind the curtain', hmm?" McKay asked, looking at his team leader with what was as close to a glare as Sumner had ever seen McKay assume towards him.

"Until we have further evidence suggesting that it's a person rather a machine behind that curtain, yes," Sumner replied, as he sat back down in his chair, the rest of his team soon following his example.

He might acknowledge that McKay had reason to be paranoid- the incident with the Genii was still fresh in their minds, after all-, but he wasn't going to ruin a potential alliance just because he was 'twice shy', as the old saying went.

All they had to do was wait, and, if things went as well as he hoped they would, they'd be heading back to Atlantis with a new ally and a secure place to evacuate any refugees they encountered to…

* * *

"Colonel?" Chaya's voice said, forcing him to blink himself back to consciousness; Chaya and the monks had taken so long doing… whatever they were doing… that he'd started to at the very least doze slightly while he waited

Shaking the last bits of sleep from his mind, Sumner stood up from the bench and turned to look at Chaya as she walked down the stairs towards them, the rest of the team following his example.

"We have relayed your request to our divine mother," Chaya began, looking apologetically at him, "and though she does not doubt the righteousness of your mission. I am afraid she cannot countenance any other people but hers settling here."

"And you really had to… _chant_ all that time to come up with that?" McKay said before Sumner could say anything himself, his tone clearly conveying his frustration at how long they'd been forced to wait only to learn they were getting nothing out of it.

Sumner only barely managed to stop himself rolling his eyes in frustration at his teammate's attitude. He might not like the fact that they'd been turned down himself, but he would have at least tried to be more diplomatic about it; how were they ever going to change Chaya's mind if they acted _that _dismissively of her beliefs?

"Is there any way we can ask Athar to reconsider?" Teyla added, walking forward to stand between Chaya and McKay; hopefully the Athosian would be able to improve the mood of the situation.

"Athar understands and sympathizes," Chaya said, looking apologetically over at Teyla. "These Wraith are a scourge among our stars, but she _has_ to place the lives of her people first."

"Well," McKay said as he stood up, "I think we both knew what you were going to say long before you even went in there."

"We prayed for Athar's guidance," Chaya said, declining even to look at McKay as she spoke; Sumner only needed to look at her face to recognise that she was angered at McKay's attitude.

"And what did Athar say?" McKay countered. "You're hiding behind your religion to justify your complete and utter selfishness-"

"Rodney…" Teyla said, turning to look in exasperation at her teammate.

"If Athar existed she would be ashamed of herself," McKay continued, either not registering or not caring about the way that Sumner and Teyla were both looking at him like they wanted to punch him.

"We ask only to be left alone, and in peace," Zarah suddenly cut in, his voice far more rapid than the more relaxed appearance he had presented earlier; it was as though he wanted to make his position clear and then end his involvement in the conversation.

"So," McKay said, looking briefly upwards to convey his disdain for the latest news, "untold thousands, possibly _millions_ of people, will die out there when they could have been saved, all in the name of Athar; how very very _peaceful_ of you!"

"You should be grateful to Athar," Chaya said, her voice low as she continued to refuse to look in McKay's direction; it hardly took an expert to know that she was extremely annoyed at his attitude.

"This is a waste of time-" McKay began.

"Athar regrets that she cannot help you," Chaya cut in, looking apologetically over at Sumner. Whether she simply disliked hear McKay insulting her beliefs, or wanted the scientist to stay quiet for reasons of her own, Sumner wasn't sure and wasn't inclined to guess; there was a reason that Teyla was the team diplomat, after all.

"And I'm sure those were her _exact _words-" McKay began.

"Rodney, that is _enough_!" Teyla yelled, glaring briefly over at the Canadian before she turned back to look at Sumner. "Colonel, if I may…?"

"That's what you're here for," Sumner said, nodding briefly in acknowledgement at Teyla's request before he turned back to look at McKay and Ford. "OK, you two with me; Teyla, join us in a minute or so."

"Hold on; why do _I _have to leave-?" McKay began.

"Because you're not helping," Sumner replied simply before he looked over at Ford. "Lieutenant?"

"Yes sir," Ford said, shooting McKay a brief look that made it clear he disapproved of the scientist's attitude as well before he walked off, Sumner and a clearly still-frustrated McKay close behind him, leaving Teyla alone with Chaya and the priests.

* * *

Glancing around the temple interior as her teammates departed, Teyla wasn't surprised to see that Chaya had walked off to one corner of the room as the three men departed; evidently, even such a person as Chaya required a little time to herself after a confrontation with McKay like the one that had just taken place. Walking over towards where Chaya was standing, the Athosian leader waited for a moment to give the high priestess time to relax after McKay's accusations before she spoke again.

"I… apologize for Doctor McKay's… comments," Teyla said, wishing she could sound more confident about what she was about to say; she was used to dealing with difficult diplomatic situations, but rarely had she been forced to work with someone as… abrasive… as Doctor McKay could be.

"He acts only in accordance to his beliefs, as do we," Chaya replied simply, as she turned around to look back at Teyla; the other woman was grateful to see that, while McKay's comments had clearly annoyed the high priestess, she nevertheless still appeared willing to talk to her.

"Doctor McKay can be… difficult… but he is correct about one detail," Teyla said; Colonel Sumner had recruited her to his team for her diplomatic skills, and she was determined to do what she could to justify his decision. "This is about a great number of innocent lives facing peril. Eventually, the Wraith shall come to the city of the Ancestors, and when they do so- "

"Your Colonel Sumner is a warrior; surely he and his men will fight?" Chaya cut in, a curious expression on her face as she looked at the other woman.

"They will _try_ to fight," Teyla admitted, nodding in confirmation of Chaya's assessment of Sumner- as much as he could frustrate her at times, he was indeed a good commander- before she continued. "However, the odds against us… even with the aid of the Phantom…"

She shook her head briefly at that comment- referring to the Phantom at a time like this would only make the situation more complicated if Chaya asked for more information- before she continued. "Well, they are… significant, to say the least; we-"

"The Phantom?" Chaya asked, looking at Teyla in what the Athosian could have sworn was a brief expression of surprise, before it faded from her face once again. "Forgive me for being impolite, but who is… the Phantom?"

"He… it is simplest to say that he is a great warrior who has done much to oppose the Wraith and dwells among us on Atlantis, although we do not know where his precise dwelling is located; his interaction with us is… complicated," Teyla said, before she shook her head slightly and looked more earnestly at Chaya. "As I was saying, we would be grateful if you could ask Athar to contemplate the prospect that, though we come from far away, we… we are all still the same people; Athar may consider us… distant relatives, if you will…"

For a moment, Chaya simply stood in silence as she studied Teyla, a thoughtful expression on her face, before she nodded slightly as though having come to a decision.

"Your words are… compelling, Teyla Emaggan," she said, smiling slightly at the other woman. "May I… see your city?"

"For what purpose?" Teyla asked, already wondering how Colonel Sumner would react to such a suggestion; if it would help them secure an alliance, Teyla had little doubt that Sumner would consent to allowing an offworld visitor into the city, but she had little doubt that he would want to take a significant number of precautions.

"If I am to appeal to Athar on your behalf, it would be… easier… if I had the opportunity to see your people on their own planet," Chaya replied, clearly taking just as much care with her words as Teyla was taking with hers. "Once I learn more about you, Athar might be more easily… persuaded… to provide you with assistance."

"I must speak with Colonel Sumner before I can confirm such a visit, but I have little doubt that he will be willing to grant you access to our city," Teyla replied, nodding politely at Chaya's request.

She would need to take care about how she phrased it when talking to Sumner, of course, but she had little doubt he would accept; it would hardly be impossible to arrange a tour that would show Chaya much of Atlantis while avoiding any of the essential systems such as the location of the Zero Point Modules.

"This is acceptable," Chaya replied with a brief nod.

"Chaya?" Zarah said, walking over to look anxiously at the younger woman; Teyla had been so caught up in trying to convince Chaya to help that she had almost forgotten the priest was still there. "Please… you cannot leave…"

"Athar is with us always," Chaya said, her tone soothing as she reached out to take Zarah's hands in hers, looking comfortingly at him as she spoke. "No matter where we are, Zarah."

As Teyla looked at the two of them, she was surprised to feel a brief, but strong, wind suddenly blow against them- it had not appeared  
Chaya placing a hand against Zarah's chest as she looked at him in a manner that reminded Teyla of Elizabeth when she was refusing to back down on some matter.

"I understand," Zarah said, stepping back from Chaya, smiling briefly at her before he walked off, leaving the two women alone in the temple as Chaya turned back to face Teyla.

"I am ready," she said simply.

* * *

Elizabeth had to confess, of all the occurrences she had been expecting to take place as a result of this latest trip through the Stargate, learning that Sumner had decided to bring a guest back to Atlantis to negotiate an alliance was one of the greatest.

She was, of course, grateful to see that Sumner had taken her past comments about giving people a chance to prove themselves rather than automatically assuming the worst of them just because of his own preference for the rules, of course, but she still had to confess to a certain amount of surprise when she was introduced to Chaya Sar, High Priestess of Athar, in the middle of the gateroom after the team had disembarked from the gateship.

"Welcome to Atlantis," she said, shaking Chaya's hand with a broad smile.

"Thank you," the other woman replied, nodding back at her.

"I hope you don't mind," Elizabeth continued, looking apologetically at the new arrival, "but our doctors do require a medical exam of all off-planet team members- and our visitors-, but after that, perhaps you would like a full tour?"

"I would love that," Chaya replied with a smile of her own.

"I have already volunteered to do so," Teyla added.

"Thank you, Teyla," Elizabeth said, nodding gratefully at the Athosian; if she wanted someone to help a potential ally get past their initial uncertainties about the expedition, she couldn't think of a better person to do the job that Teyla. "If you would just follow Teyla to the infirmary, Chaya…"

"Of course," Chaya said, nodding slightly at Elizabeth before she turned to look at Teyla. "Please, lead the way."

"Maybe I should tag along," McKay suddenly cut in as the two women turned towards the nearest corridor. "You know, in case you have any questions Teyla can't answe-"

"I am certain that Chaya and I will be fine, Rodney," Teyla cut in, holding up a hand to halt the Canadian as she and Chaya walked off towards the infirmary.

"There are a lot of systems you know absolute-" Mckay began, before Sumner grabbed his arm, prompting him to look in the colonel's direction. "_What_?"

"I somehow doubt that Chaya will wish to know more than the essential details of Atlantis's technological capabilities," Sumner said, glaring pointedly at McKay as he addressed the Canadian in a low voice. "We're trying to give her a good impression _culturally_, not show off how advanced we are technologically; your expertise is _not _required in this matter."

With that said, he stepped back to turn and face Elizabeth. "If you'll excuse me, Doctor Weir, Lieutenant Ford and I have some things to straighten out; I need to oversee the current training program with those Wraith stunners we acquired, and I have a few reports I need to go over myself."

"Of course," Elizabeth replied, nodding briefly back at her military commander before he and Lieutenant Ford walked off in one direction while Teyla and Chaya vanished down the corridor leading to the Atlantis infirmary, leaving Elizabeth standing alone with the Canadian scientist.

"So," Elizabeth said after a moment's silence as she turned to look at McKay, "since Colonel Sumner has other matters to attend to, shall I assume that you'll be willing to fill me in on the full details of what took place during this mission?"


	23. I Will Stand Up For You

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Usual rules still apply to this kind of chapter; whatever you don't see here, such as Chaya's brief conversation with Doctor Beckett in the infirmary, or Elizabeth's meeting with Chaya to discuss the possible treaty for Proculus, happened pretty much exactly the same way as it did in the series (Barring the obvious exceptions that you'll doubtless realise when you read this)

The Phantom of Atlantis

"Where are we at?" Elizabeth asked as she looked inquiringly at her chief scientist as she walked out of her office- she always liked to get a little exercise when she was talking with some of her staff about something that didn't need to remain confidential or private; it was the only real way to get any kind of exercise in Atlantis-, McKay close behind her, his recent report on the events that had taken place on Chaya's planet still fresh in her mind.

She had to admit, she could see how Sumner had been convinced to change his usual policy on bringing visitors to Atlantis; if they could convince Chaya to provide some of the more primitive peoples of the Pegasus galaxy with sanctuary, even without the obvious benefit of having a planet on which to establish an Alpha Site, they would have simultaneously succeeding in saving lives and depriving the Wraith of a potential food source. Transport would have been difficult, of course, but the puddle jumpers could hold a surprising amount of people, and there was always the possibility of finding a crashed dart or something that they could use to 'scoop' some natives to transport them there in less time…

"Either she knows where the weapon is and she's playing us," McKay said as the two of them walked out of her office into the control room, drawing her attention back to the matter at hand, "or she has no idea, in which case we are wasting our time."

"So… what do you suggest?" Elizabeth asked, as she looked uncertainly at McKay while trying to determine what he was going to say next.

"Take another team back in the jumper and scan the planet for energy signatures," McKay replied, as the two of them walked down the stairs towards the main gateroom. "Chaya's people won't have a clue what we're doing from orbit unless they are a technically advanced race which are pretending not to be…"

His voice trailed off, evidently recalling their previous encounter with that very same situation during their first encounter with the Genii.

"Which has happened before…" he admitted, looking uncomfortably over at Elizabeth; the obvious occasion of their prior encounter with the Genii still weighted heavily on Elizabeth's mind, particularly given how close she herself had come to being shot or abducted if it hadn't been for the Phantom's intervention at the last minute.

"Did you find anything abnormal?" Elizabeth asked at last; after she'd spent so much time making sure Sumner remembered that he couldn't accuse the Phantom of anything without evidence, she wasn't going to allow any other members of the team to get away with the same thing in a different situation. "I mean, something that would suggest they _are_ more advanced than they claim to be?"

"No," McKay said, shaking his head promptly. "They're either, uh, pathetically _pre_-technological or brilliantly _post_-technological."

"And there's no way this can be a natural phenomenon?" Elizabeth asked, looking inquiringly at the Canadian.

"A perfectly timed, directed energy burst that only affected the _Wraith_ ships?" McKay replied pointedly.

"That's a no?" Elizabeth said; she was fairly certain McKay was saying that was the case, but with his usual sarcastic manner there was no way to be entirely certain.

"That's a no," McKay confirmed with a brief nod.

Elizabeth sighed slightly in frustration as she looked at the ceiling.

What _was _it about the Pegasus Galaxy that prevented her from encountering the simple situations? Not only did she have to deal with an at-least-_slight _interest in a figure who may or may not have an ulterior agenda while simultaneously possessing a clearly extensive knowledge of the city and how everything within it worked- as well as being able to control it to a greater degree than anyone on her team had displayed the ability to accomplish-, but now, when they _finally _discovered a potentially valuable ally, they had to deal with the fact that the society in question might be keeping something from them about how they came to be in that position in the first place…

"_Doctor Weir_," Carson's voice suddenly said over the radio, breaking into her train of thought. "_I have those results_."

"Thank you, Carson," Elizabeth replied, as she and McKay stood up. "We're on our way."

As the two of them walked out of her office, Elizabeth could only hope that this part of the meeting would answer at least some of their questions about Chaya's planet; if she was going to meet Chaya to discuss anything about an alliance, she would prefer to have more information than what they had currently available to her if she was going to think of something they could offer Chaya in exchange for her providing them with sanctuary.

* * *

A few hours later, as Chaya sat in the room that had been allocated to her, Teyla currently sitting outside the room with a guard- Elizabeth had made it clear that it was only policy to keep an eye on visitors, and Chaya understood that it was not intended as a personal criticism-, studying the information provided for her by Earth's databases, she couldn't help but wish that things could be different.

She disliked lying to Doctor Weir, of course, but she had no choice if she wished to keep her true identity secret from these people; her exile to her world was difficult enough as it was.

If only she had been strong enough to reject Teyla's last attempt to plead the expedition's case…

But, when the Athosian woman had mentioned that the Phantom dwelled in Atlantis- even if his location in the city was not public knowledge-, Chaya had known that she _had _to return to the city, if for no other reason than to try and meet the man whose very name struck fear into the hearts of the Wraith whose minds she had read when they attempted to come to her world in the past.

He had revived the legacy of her people, using their technology against the enemy that had defeated even them, waging a one-man-war against the entire Wraith species for apparently no other reason than that he had the ability to do something and had chosen to do it…

It was… gratifying, was the best term that she could think of… to see someone willing to use her peoples' technology in the manner that her people themselves refused to use the powers they had acquired after Ascending; even when faced with people they knew dying, so many of her kind had simply 'sat' back and watched after they had Ascended, refusing to interfere with the affairs on the universe even when they had once walked among them.

When faced with the possibility of meeting a man who used their technology to take actual _action_…

She was only slightly ashamed to admit that she'd been too weak to resist the temptation; after she herself had been unable to do more to the Wraith than annoy them by keeping a single world out of their hands- no matter how dear that world was to her personally-, the possibility of meeting someone who had done enough damage to them to inspire the fear she had sensed as she banished them from her planet…

"Interesting reading, isn't it?" a voice said from behind her.

Jumping up in surprise at the interruption- she had 'turned off' her 'awareness' of her surroundings while reading so that she would avoid attracting further suspicion if someone visited her while reading and wondered why she showed little surprise at their presence; the less people knew about her the better-, Chaya turned around to look in the direction that the voice had come from, only for her eyes to widen as she saw who was standing in one corner of the room.

She had little idea how he could have gained access to the room- it had been many years since she had lived in Atlantis, and she had never been one to be particularly concerned about the city's architecture-, but even as he stood in the shadowed corner of the room, his silver mask made his identity obvious.

"You are the one whom Teyla called… the Phantom, I assume?" Chaya asked, raising a curious eyebrow as she stepped forward slightly to look at the man before her better.

"I am," the Phantom replied, inclining his head slightly in response as he looked back at her. "And you are Chaya Sar, officially here as the High Priestess of Athar on the planet Proculus, correct?"

"Correct," Chaya replied, before she registered what he had just said to her. "What do you mean, 'officially here'?"

"Come now, I think we are both aware that you're not _exactly_ a normal priestess," the Phantom replied, smiling slightly under his mask as he looked at her. "I may have never visited your planet myself, but I _have _had a great deal of opportunities to study the Ancient database; your world is officially listed as being 'protected' by one of the 'Higher Ones'- the term they used to refer to those who mastered Ascension ahead of the rest of your people-, you feel comfortable enough to make decisions that can affect the future of your entire planet, you possess the Ancient gene at a level that surpasses any of the expedition, and you display little surprise at my presence and appearance despite the fact that you could not possibly have heard of me before Colonel Sumner's team arrived… unless, that is, you are an Ancient who has read the minds of the Wraith who have come to your world in the past to learn about the state of their occupation of this galaxy before you send them packing. Am I correct in my deductions, or am I not?"

After a moment's silence, Chaya smiled slightly at the man before her.

"Your reasoning is correct, Phantom," she said, before she tilted her head to one side as she smiled a little at him. "Or would you prefer it if I referred to you as 'John'?"

"Either is fine with me, really; I've gone by 'the Phantom' for so long I sometimes forget that I ever had a name before it," the man before her replied, smiling slightly at her once again before he assumed a more serious expression. "Of course, if you have some objection to my chosen alias, you may call me whatever you wish; I simply assumed it because-"

"It is… fine," Chaya replied, raising her hand to halt him mid-sentence, smiling reassuringly at him. "You are not one of my people, true, but you have done their legacy great honour in your actions against the Wraith. I have sensed the thoughts of the Wraith who have come to my world since you came to this galaxy, and always they have made it clear that they fear you, in many ways more than they even feared my people."

"Hold on; the Wraith fear _me _more than they feared the _Ancients_?" the Phantom- for some reason Chaya 'sensed' he preferred her referring to him by that name rather than 'John'- said, a slightly proud-yet-embarrassed smile on his face. "Uh… glad I've made that kind of impression, but how did I get them _that _scared?"

"Why should you not?" Chaya replied, a slight smile on her face as she walked closer to him. "You leave little to no clue of your history even among the people you help, you come out of nowhere years after my people left this galaxy, and you rely on significantly different tactics to what we attempted in the past; you combine what the Wraith know and understand about my people with tactics and strategies that they do not. The Wraith do not know what to make of you; after fighting us for so many years while remaining aware of what we were capable of and how we thought, _that _makes them fear you more than any physical weapon you might possess."

"Ah," the Phantom said, smiling slightly back at her. "Well, it's always good to feel appreciated."

"Yes…" Chaya replied, a slightly wistful tone in her voice, prompting a concerned look from the Phantom.

"Problem?" he asked, looking curiously at her. "I mean, you don't exactly _look _like you're having the time of your life…"

"It is…" Chaya began, sighing slightly as she turned away briefly before she looked back at him. "I suppose it is simply… refreshing… to have met someone who knows how it feels to feel alone."

"Alone?" the Phantom said, stepping forward slightly as he looked at her in surprise. "What are you _talking _about; you live among your people-"

"None of whom are aware of the true extent of my powers and status," Chaya clarified, looking at him with a slightly saddened expression on her face. "You have lived alone since you came to this galaxy, but I have lived more than alone; I have lived what is essentially a _lie _for the last several thousand years, simply so that I might remind myself of the reasons I chose this course of action, and I am still forever isolated from the people I have dedicated my existence to protect…"

She sighed slightly as she looked back at him. "You might live alone, but you have at least been able to be true to who you are; your only lie is to not correct an assumption, which is a minor deception in the grand scheme of things."

The Phantom smiled slightly at her.

"Thank you," he said simply.

"You are welcome," Chaya replied.

Then, before the Phantom could react to her last statement, Chaya leaned forward and kissed him, her lips neatly avoiding the edges of his mask as they met his. She noted a slight twist around the right corner of his mouth, as though he was smiling slightly, but shook that impression off; it seemed more like a natural part of his appearance from what she could feel of it…

* * *

Elizabeth wasn't sure which one was more frustrating any more; Chaya's refusal to even consider most of the more obvious things that the expedition had to offer- religious knowledge was promising, but she still wished she could offer Chaya something more substantial than that-, or McKay's continued insistence in finding something suspicious about her.

"You want to send her back?" she asked, shaking her head slightly as she walked towards the stairs leading to the control room. Why was it that at least _half _her senior staff seemed to have become conspiracy theorists since they'd arrived in the city? She'd just spent a few moments checking on the Athosians' current status with Teyla- so far they were settling in and rebuilding fairly well in the aftermath of the recent storm-, only to run into McKay as she began to walk back towards her office as he demanded for Chaya to be sent away from Atlantis.

"All I know is she's not who she's pretending to be," McKay replied, keeping pace with her as she walked up the stairs.

"You know this _because_?" Elizabeth countered, not even looking behind herself as she continued to walk; if McKay had genuine reasons a brisk attitude wouldn't stop him revealing them, but if he was just being paranoid she was giving him as good a reason as any to stay silent.

"What?" McKay asked, sounding offended at the question. "I'm not allowed to have intuition?"

"You?" Elizabeth asked, as she briefly turned to shoot him a sharp look even as she continued to walk. "No."

"Oh," McKay said simply.

"I asked Teyla to keep an eye on her while Chaya's conducting her research into our religious history," she added as she continued walking; she could only hope that the last statement would be enough to convince McKay to stop trying to look for a threat where none existed.

"Look," McKay countered, as he continued to walk after her, "no offence, but Teyla's still new to this whole thing; she wouldn't know what to really _look _for."

"Do you mind explaining what Teyla's expected to be 'looking' _for_?" Elizabeth asked, continuing to walk despite her own inner curiosity; so far McKay hadn't given her any information that could actually justify his own apparent paranoia where Chaya was concerned.

"Look, the biometric differential rate between her and us is not insignificant Elizabeth!" McKay insisted. After a few seconds of silence- evidently he had been waiting for Elizabeth to say something before realising that she wasn't going to-, he spoke again. "What I'm saying is, _the woman set off an alien alarm_!"

"Come on," Elizabeth sighed, as she finally turned to look directly at her chief scientist, "you don't _know_ that for certain. Besides, Grodin told me that you are nowhere _close_ to understanding what the nature of that device is-"

"There are too many _unknown_ variables," McKay countered, one hand jabbing slightly forward as though he was trying to better emphasise his point. "There's the energy weapon we saw in action, the fact that they claim never to have seen the Wraith… what about the fact that she's essentially a _textbook_ case of healthy?"

"All _very_ mysterious, yes," Elizabeth sighed, as she turned around to walk into her office, checking over the paperwork that had accumulated there since she had left for her brief walk. "But what does it _prove_?"

"That we should give her a one way ticket back home," McKay replied simply, his tone suggesting that, as far as he was concerned, it would be for the best if they never saw Chaya again.

Elizabeth couldn't believe it; had she been _that _accurate in her assessment of Atlantis having turned her senior staff into conspiracy theorists?

"There is obviously something very… _different_ about her, yes," she admitted, as she walked out of her office, her electronic notepad in her hand as she looked at the scientist. "But that doesn't necessarily make her a _threat_-"

"It doesn't rule it _out_, either," McKay countered, his expression giving Elizabeth the impression that even her brief admittance of the differences between Chaya and them were all that he had been looking for.

"Until we know otherwise," Elizabeth continued, returning her attention to the notepad as she walked past McKay, "for the moment, I think what we can _gain_ by securing a treaty is worth the risk of her being here."

With that, she turned around and walked into her office, leaving Mckay staring silently after her as she closed the door behind her.

_At least _that's _been dealt with_, she reflected to herself as she sat down behind her desk, pulling out the next batch of reports as she began to study them. _Now maybe I can get these files out of the way_…

She just wished that she could escape this nagging doubt that there _was _something about Chaya that she should be concerned about, regardless of how much effort she'd put into arguing that Sumner and McKay allow her to remain.

She didn't agree with McKay's apparent belief that she was a threat just because she wasn't entirely human- the SGC had encountered too many fundamentally benevolent alien races for her to believe that something would automatically attempt to attack them just because they weren't the same species-, but that still didn't account for her feeling that their new visitor was not quite the peaceful, religiously-inclined ambassador that she appeared to be.

Plus, there was that frustrating feeling in the back of her mind that she should be… _jealous _of the woman for some reason that she couldn't quite put her finger on…


	24. Unlike Any Other, In Her Eyes

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

For a moment, as Chaya's lips met his, the near-instinctive powers granted to her by her Ascended status manipulating his senses in ways he was certain were instinctive, John could almost believe that he was kissing another woman, a woman with paler skin and shorter hair…

But, as much as he wished it was otherwise- as much as he wished that he could genuinely experience the 'reward' that he would regard it as to genuinely kiss the woman who had given his life meaning so long ago- the illusion was just that; for all its detail, it was still an illusion.

He didn't even hesitate; as soon as his brain had been given time to process what had happened, John had stepped away from Chaya, shaking his head resolutely even as he looked regretfully at her.

"_No_," he said simply, raising one hand as Chaya looked at him with a slightly surprised expression; rejecting someone as powerful as she was might not be the _smart _thing to do, but it was what John felt he _should _do. "I…"

"You cannot do this," Chaya said, her tone giving no trace of how she might feel about that fact as she looked back at him.

Somehow, he wasn't sure if that made it better or worse. As much as he appreciated her apparently being so understanding about his reaction, he'd almost have found it… _easier _to relate to her if she'd been more obviously angry at him; he'd grown 'used' to reacting to _that _kind of response after years of fighting for his life…

"Yeah… I can't," John replied, shaking his head apologetically as he looked back at her. "You're… well, you're a very… _interesting _person, don't get me wrong- you're the first Ascended _I've _ever met in this part of the galaxy, I'll tell you that for nothing-, it's just that… well…"

He trailed off, uncertain how phrase what he was about to say- he wasn't used to talking with _anyone _about how he felt; it had been so long since he'd had any kind of conversation that wasn't either bantering with the Wraith or discussing recent battles-, but Chaya, evidently sensing his discomfort, finished the sentence for him.

"There is another in your life," she said simply.

John sighed in relief.

"Yeah…" he confirmed, nodding at her assumption. At least he didn't have to worry about figuring out _what _he was going to say to her about his feelings; as much as he tried to talk it over in his 'conversations' with the body of the elder Elizabeth, he still found it hard to really _say _how he felt about Elizabeth to anyone but himself. "There _is _somebody else. She doesn't know I _feel_… that way… about her, of course- hell, it's… well, 'complicated' isn't even _close _to being the word for it; you'd need a term _way _bigger than that to describe this whole mess- and she might not even feel the same _way _about me… but…"

"I understand," Chaya said, an understanding smile on her face as she looked back at him. "You are aware of what I am… capable of… as I am, and yet you would still wait for she whom you care for when you do not even know if she reciprocates your love?"

John smiled slightly.

"Might seem crazy, I know, but that's me all over; a bit of a glutton for punishment when it comes to emotional issues," he said, forcing a slight chuckle before he assumed a more solemn expression. "Besides… well, I know enough about Ascension to know what you're probably about to suggest we do- had a _lot _of time to read on my hands while I was here-, and I just… I can't…"

He sighed. "I can't… I can't give _you _what you'd give _me_ if we… did _that_. I already-"

"You have already given her everything, even if she does not know it," Chaya finished for him, her smile growing softer as she looked at the man before her. "You truly do love her, don't you?"

John simply stared silently back at Chaya for a moment, fully aware of how evident his discomfort was when discussing this particular topic while equally aware that the woman before him would see through any kind of lie he might tell.

"She… she saved me," he said finally, shaking his head slightly as he looked back at her. "It's… hell, she gave my life _meaning _when all I had was nothing; it's kind of hard for me _not _to love her after all that."

Chaya smiled once again.

"You are… fortunate to have someone like her in your life," she said, looking at him with an understanding expression, before she sighed slightly. "I only wish that I could do more for you…"

"'Do more'?" John repeated, looking curiously at her. "What do you mean by that? I mean, from what I heard you saved Colonel Sumner's team and pretty much _vaporised _a couple of Wraith darts; it doesn't seem to me like there's much you _can't _do-"

"While I am permitted to defend Proculus by the Others, I can take no action in the defence of those not of my world; if any other people came to my world, the others would stop me from taking action," Chaya explained, looking regretfully at him. "While the expedition's goals are doubtless commendable, and Doctor Weir and yourself have shown me that you genuinely wish to help others in this galaxy, my people would never permit it. I can offer you and these people nothing more than what I have done already; even simply saving Colonel Sumner and his team from the Wraith Darts was pushing the limits of what I am permitted to do. I cannot offer the expedition anything more than what I have already."

"Ah," John said, nodding briefly in understanding as he looked sympathetically at her.

He had to admit, in that context, he understood how he could probably be seen as having the better end of the deal right now. He might have spent the better part of the last few years with only himself for company- the Wraith he killed hardly counted, and the only times he met other humans were brief visits where he never dared to stay long in case- but at least he was able to actually _take _action whenever and wherever he wanted to do it.

It wasn't much, he freely admitted- twenty years of training and only five Wraith hive-ships to show for it; not exactly the stuff that legends were made of, in his opinion-, but at least he could do _something_…

"Well," he said at last, as he indicated the corner of the room where he had entered- really, it was _amazing _the amount of secret passages were available for the inhabitants' use in Atlantis once you know they were there-, "I'd best be off; can't exactly stay in one place too long, you know."

"Must you remain?" Chaya asked, looking quizzically at John.

John blinked.

"Well… I don't _exactly _have much choice," he said, looking uncertainly back at her. "I mean, the Stargate's not exactly that accessible now…"

"There are… other means… by which you could depart," Chaya said, taking another step towards him. "I have seen the time you spent among those my people provided sanctuary for… you are aware of how to accomplish it-"

"_Not _happening," John countered, stepping back from her as he vehemently shook his head. "It's a nice idea, don't get me wrong, but I'm just… that's not my thing, really; sitting around and contemplating my own enlightenment?"

He shook his head grimly. "Even if I can't take any direct action right now, I can still take _some _action by helping these people; that's more than I could do if I did… _that_."

"And, again, you could not be with her if you took such an action," Chaya said.

John sighed.

"Y'know, _this _is why telepaths make me uncomfortable; you make everything sound so… _selfish_," he groaned as he looked at her.

"On the contrary," Chaya replied, smiling reassuringly at him. "You forsake access to ultimate power because, at heart, you recognise that you do not desire it; you do not seek to have power, but simply seek to be worthy of she whom you love."

For a moment, John simply stood in silence, reflecting silently on what Chaya had just said to him, before he smiled back at her.

"Well… that sounds better than what I said earlier," he said, nodding slightly at Chaya in gratitude. "Thanks."

With that, he turned around and began to walk back towards the corner where he had first appeared within the room, pausing briefly to turn back and look at Chaya one last time. "Sorry I can't do anything more for you than listen."

"On the contrary," Chaya replied, smiling slightly at him reassuringly. "It has been… refreshing to talk to you."

For a brief moment, the man who was seen by the Pegasus Galaxy as the closest thing they had seen for the last ten thousand years to an actual Ancient simply stared silently at the first living example of that species he had ever met, his eyes silently reflecting her gratitude at this brief conversation the two of them had shared…

Then, with a brief nod, John turned around and vanished into the shadowed corner, his black cloak concealing him from view as he ducked down into the small passage that connected him to the city's secret passages.

He'd meant what he'd said; it _had _been… nice… to talk to someone who knew what it was like to be alone.

But, in the end, nothing could ever _really _have happened between them; even if she hadn't been a being of pure energy, his heart was just…

As pathetic as it might sound, he'd already met his perfect woman, and he just could _not _love another until his love for her had ended, which was looking increasingly like it wouldn't.

If her apparent interest in medical doctors couldn't stop it- the 'first' Elizabeth had told him all about her engagement to a guy called Simon Wallace back on Earth; he'd just generally not thought much about it because, in all fairness, how serious could the relationship have _been _if she'd left him behind like that?-, he somehow doubted that _anything _could stop him feeling the way he felt about Elizabeth Weir…

* * *

There were times when Elizabeth realised that her approach to her temporary duty as head of Stargate Command had left her woefully unprepared for the reality of the situations that she would subsequently encounter when put in charge of Atlantis; at the time she'd been so focused on trying to arrange a diplomatic solution to the problem of the Goa'uld that she'd completely shut down all regular Stargate activity, thus leaving her with nothing to focus on but the negotiations.

Even with Doctor Jackson helping her to better understand the Goa'uld mentality, her time at the SGC had simply consisted of trying to talk to an alien race who fundamentally had no interest in anything other than conquest; other than that, after the initial crisis of Anubis's attack was over all they had to worry about was making sure the Goa'uld didn't try anything.

Here in Atlantis, on the other hand…

When Elizabeth saw Doctor McKay walking towards her office, she knew even before he started speaking that the situation with Chaya was only about to become more complicated.

"You _have _to see this," he said as he walked into the office, once again displaying the same 'getting-to-the-point' attitude that Elizabeth was never certain how she felt about.

"Did you sleep last night?" she asked as she looked critically up at the Canadian, even as she stood up; if McKay wanted her to see something, she might as well get it over with now and spare herself the hassle of dealing with it later.

"No," McKay replied; Elizabeth wasn't sure if she should feel worried or relieved that he actually sounded excited about something as he walked through the control room towards a laptop connected up to an Ancient console.

"This is the data from the biometric sensors," the Canadian scientist continued, evidently declining to elaborate on the reasons for his lack of his sleep, as he sat down in front of the laptop. "I can't tell you exactly what all these signatures mean, but look at this."

As Elizabeth bent over his shoulder to better study the screen, he indicated two readouts displayed before him, one of them a simple waving line while the other one displayed what looked to Elizabeth like multiple lines following a similar pattern on a larger scale.

"These are ours," McKay continued, indicating the lower line before his finger moved to the upper set of multiple lines, "and _this_… this is hers. There's a _distinct_ difference."

"She _was_ born on another planet in another galaxy…" Elizabeth pointed out, trying to conceal her frustration. Why was it that at least _half _of her senior staff seemed determined to find fault with people whose only 'crime' seemed to be a desire for privacy or secrecy? It was hardly like it was illegal to keep things quite when you didn't even know everything about the other party; just because they'd had one bad experience with the Genii shouldn't colour their perceptions of _everyone _in this galaxy…

"They're different from Teyla's too," McKay said, cutting off that possible line of defence before Elizabeth could take it any further.

"That doesn't mean-" she began, hoping against hope that she could say something that would make Mckay see reason.

"Elizabeth," he cut in, turning to look at her as he spoke in a low voice, "she's not what she seems to be."

"I sense nothing but a very honest and spiritual person," Elizabeth said, as she looked pointedly at McKay. She was starting to realise how tough it must have been for General O'Neill to convince the program to accept Teal'c during the early days of the SGC; why was it that there were always at least _some _people who worried that everything that wasn't human would automatically turn out to be a threat?

"Alright," McKay said after a moment's pause, "there may be a way to find out. You're opening negotiations with her this morning, right?"

Elizabeth nodded, already wondering where the scientist was going with this new line of questioning; right now, she just hoped that it would be something that would at least satisfy him without giving Chaya the wrong impression.

"OK," McKay continued, "well, let me sit in. I'll pretend to be taking notes on the laptop when really I'll be scanning her for any anomalies: radiation, EM scans, energy signatures. That way, if I _am_ crazy, you and I are the only ones who need to know. What's the harm?"

After staring silently at McKay for a few moments, Elizabeth nodded in resignation.

"All right," she said, nodding briefly at him. "Just remember; be discreet."

"Hey, I'm _Mr _Discreet!" McKay protested, looking indignantly at her.

"Also," Elizabeth continued, folding her arms as she looked pointedly at McKay, deciding to ignore that "_don't _jump to conclusions just because she isn't 100% human; if that machine was just letting us know that she's not like us without actually identifying her as a threat, you could jeopardise our attempts to establish a treaty."

"What?" McKay said, looking in confusion at her. "But… Elizabeth, if she _isn't _human-"

"Given that we haven't expressly _asked _her 'are you human?', it's perfectly possible that she's simply a species with a physical resemblance to humans who is unaware that she's different from us in some areas," Elizabeth pointed out, continuing to glare at McKay as she spoke. "The SGC has encountered more than one non-human race who turned out to be perfectly friendly once any initial misunderstandings had been cleared up; you can clarify whether or not Chaya's human if you want, but you are _not _to assume she's a threat if the answer is 'no' without further information. Is that clear?"

"Crystal," McKay nodded.

* * *

As Elizabeth sat in the conference room opposite Chaya, Teyla and Colonel Sumner sitting on either side of their visitor while McKay sat opposite her, she could only hope that McKay remembered to do what she'd told him and avoid freaking out if his scans confirmed his theory that Chaya wasn't human. She might understand his reasons for concern, but at the same time she wasn't willing to encourage those under her command to judge everything based solely on the idea that it wasn't human; if they started assuming the worst of everything just because it wasn't the same species there was no telling whether it would end.

"I admit to being impressed by most of what I've read of Earth religions," Chaya said, looking around the table at the Atlantis staff gathered before her as she spoke. "The Torah, the Koran, the Talmud, the Bible; many of them reveal a diverse and deep desire to grasp the divine."

"So, we _do _have something we can offer you," Elizabeth asked, trying not to sound too eager; given the failure of their previous attempts to win Chaya's support, any kind of progress was welcome at this point…

"But I've also been reading about your history," Chaya admitted, her expression the same neutral one that gave no indication of what she was thinking as she looked at Elizabeth. "Even now, somewhere on your planet, you are at war."

"I made no attempt to hide that fact from you," Elizabeth replied, her tone remaining neutral; Chaya was at least still listening, even if her last sentence left Elizabeth with a renewed uncertainty about her chances of success. "Chaya, we are definitely not perfect."

"There's a lot about you as a people that I find disturbing," Chaya replied, remaining frustratingly neutral in her tone; if she had at least sounded somewhat distasteful Elizabeth would have had something to work with.

"Can that not be said of any people?" Teyla asked, looking uncertainly at Chaya.

"No," Chaya replied, shaking her head. "Every soul on Proculus is free from the hatred and the anger people from Earth seem to feel for each other."

"While I acknowledge that not everyone on Earth is perfect, you can hardly judge the entire species based on the actions of some," Elizabeth continued; even if Chaya's words suggested that it was unlikely she would permit them on Proculus, she had to at least make the attempt. "Besides, given our current situation Earth doesn't play a part in these negotiations. I'm not talking about Earth's inhabitants; I'm talking about every member of my expedition team _here_ in Atlantis, _and_ I'm talking about the friends we've met since coming here, like Teyla's people."

"There are some among you- yourself included, Doctor Weir- that I know Athar will welcome with open arms," Chaya said, leaning forward while briefly glancing at McKay in a manner that left Elizabeth slightly uncomfortable before her gaze shifted to Colonel Sumner. "But there are others…"

As much as Elizabeth would have liked to voice her agreement with Chaya's assessment- Colonel Sumner's military record had seemed good on paper when she'd selected him as her military commander, but his current attitude towards the Phantom's continued presence continued to frustrate her-, she knew that what Sumner had told her in the aftermath of the nanovirus had been accurate; they couldn't afford to present a disunited front at any time, particularly at such a crucial meeting as this one.

"I handpicked every member of this expedition," she said, looking resolutely at Chaya as she hoped her own doubts about Sumner weren't obvious on her face, "and I know Teyla feels as confident about her own people."

"I'm sure," Chaya replied simply.

If Elizabeth hadn't been negotiating with her she would have been impressed; it was almost remarkable how controlled Chaya could be regardless of the situation she was in or the topic of her current conversation.

"At the end of the day," she continued, hoping that this would get through to Chaya- particularly with McKay's doubts about her taken into account; maybe if she could point out the importance of trust Chaya might be more willing to talk with them about herself-, "this is a matter of trust."

"Yes," Chaya replied, nodding slightly at her. "It is, Doctor Weir."

She turned to look at McKay as he sat opposite her. "Have your scans found anything yet, Doctor McKay?"

Only Elizabeth's years as a diplomat kept her from showing how shocked she was at that latest turn of events.

Chaya _knew _that McKay was scanning her?

_Well_, she thought to herself, already regretting her decision to give into McKay's paranoia, _so much for any hope of _that _remaining a secret…_

"Um…" McKay said, looking uncomfortably as he reached up to place his hand on the lid of the laptop, closing it as he continued to look awkwardly back at Chaya. "Uh… actually, no."

"I'm sorry, Chaya," Elizabeth said, looking apologetically at the other woman, hoping that she could at least partly salvage the mess she'd made of things. "Doctor McKay felt that there was cause for legitimate concern as to-"

"Whether or not I was who I appeared to be," Chaya finished; her tone remained as neutral as ever, but her face appeared slightly dejected at this latest turn of events.

"I'm sorry, Chaya," Elizabeth said, hoping that the other woman could appreciate the sincerity of her apology. "I honestly felt it would do no harm to assure him-"

"Stop apologising, Elizabeth!" McKay yelled, standing up as he glared at chaya. "How did she know?"

"What does that have to do with-?" Teyla began.

"She's an Ancient," McKay interjected.

"She's _what_?" Sumner yelled, turning to look incredulously at the woman sitting close to him; Elizabeth had a feeling that only years of military training were allowing him to maintain enough control

"I'm right, aren't I?" McKay asked, looking pointedly at Chaya. "The perfect health, the energy weapon, the fact that she has the gene; it's the only logical explanation."

"Hold on a minute here; you're an _Ancient_?" Elizabeth said, looking incredulously at Chaya.

"I just… I don't understand the _act_," McKay continued, looking at the woman in confusion. "I mean, you must know we'd give just about anything to talk to you, to learn from you. I mean, what is it? What, are you… checking us out?"

"I see that in my desire to come to Atlantis, I have revealed too much of myself," Chaya said, declining to directly answer McKay's statement as she looked around the table.

Elizabeth couldn't believe it; how could Chaya be so… _calm_ even after they'd apparently correctly deduced her greatest secret?

"He's right?" she said, looking incredulously at Chaya.

"I'm _right_?" McKay echoed; Elizabeth had no idea how to feel about the fact that McKay had voiced a theory like that when even he wasn't entirely certain about it.

"I I _am_ what you call an Ancient," Chaya said, inclining her head. "And it is also true that I can never offer your people sanctuary. But you are only partly correct as to why I came here."

"Why _did _you come here?" Sumner asked, looking at her with a renewed intensity; Elizabeth wished that he would stop instantly analysing every unexpected occurrence in the city as though it was a potential threat rather than just something that happened.

"The Phantom," Chaya replied.

"The Phantom?" Elizabeth repeated, looking at the woman with a renewed intensity (That was _not _in any way motivated by jealousy; she simply wanted to know _how_ Chaya knew of the Phantom).

"I have heard much about him from the thoughts of the Wraith who have come to my world," Chaya explained, for the first time almost appearing embarrassed as she spoke. "When the opportunity came to find out more about him-"

"You came here because of the _Phantom_?" Sumner repeated, staring incredulously at the now-revealed Ancient with what looked to Elizabeth like an at least slightly resentful aspect. "We go to all the trouble of trying to form an alliance, and the only reason you're here is-"

"_Colonel_," Elizabeth said, glaring over at Sumner; things might not have turned out as they'd hoped, but the colonel's attitude was hardly going to help them improve things.

"Hold on; you've read their _minds_?" McKay said, looking in ever-increasing confusion at Chaya. "How-?"

"I've stayed here long enough," Chaya said, rising to her feet as she stepped away from the table, subsequently walking through the door behind her.

"Chaya!" Elizabeth yelled, getting to her feet and hurrying after the other woman, Teyla just behind her. "Wait; you can't just _leave_! Your people are the whole reason we even came…"

She trailed off as she took in the sight of Chaya standing just outside the conference room, the formerly almost impeccably-balanced woman suddenly giving the impression that she could barely stand.

"Chaya?" Teyla asked, walking up to stand alongside Elizabeth as she looked uncertainly at the other woman.

"I can't…" Chaya said, her voice suddenly weak, as though she'd suddenly run a great distance in a matter of seconds, as she held up a hand.

"Can't…" she gasped again, before she suddenly collapsed to the ground in a heap.

"Chaya?" Elizabeth called, anxiously hurrying over to crouch down beside the unconscious woman; it would be almost _ridiculously _bad luck if they lost the first living Ancient they'd come across in this galaxy so soon after discovering her. "Chaya?"

"Would it be asking too much for things to remain _consistent _here for once?" Colonel Sumner asked, as he looked pointedly down at the currently collapsed form before him, as he and McKay hurried out of the conference room to join Teyla and Elizabeth.

Before Elizabeth could even begin to form a reply- not that she had much idea what she'd say- Chaya had regained her footing and was standing up once again, looking resolutely out at something that none of them could see.

"They're coming for them," she said, apparently not even registering the presence of the others around her. "I should have never left them."

"What's going on?" Elizabeth asked, looking in ever-growing confusion at the Ancient- an actual _Ancient_!- before her.

"I'm sorry, Doctor Weir," Chaya replied, as she turned to look at Elizabeth before she closed her eyes and raised her head. "We shall not meet again."

For a moment nothing happened, and then, right before the four astonished members of the Atlantis expedition, Chaya Sar's entire body suddenly glowed a brilliant white before assuming the appearance of a brilliantly-glowing form of energy, thin tendrils 'reaching' out from all around it. For a moment, one of them came in contact with Elizabeth, and she could have _sworn _she heard a voice-

_He loves you, Doctor Weir_.

-but then the tendril vanished, leaving the energy that had once been Chaya Sar to move towards the Stargate, which promptly activated the second she reached it. Before any of the technicians could do anything, the energy- the _Ascended being_, Elizabeth corrected herself; nothing else could account for what they were witnessing- had passed through the event horizon of the Stargate before the wormhole shut down, leaving the group that had so recently been in the conference room staring at the now-empty gateroom.

"Uh… ma'am?" the technician currently on duty- Elizabeth thought that his name was 'Chuck', but she couldn't be certain- said, looking curiously over at her. "What just happened?"

Looking at the now-dormant Stargate that had just separated them from the first Ascended being they'd ever encountered in the Pegasus Galaxy, Elizabeth had no idea how to answer.

What had all that meant?

Why had Chaya suddenly decided to leave like that?

And what had that brief… _flash_… she'd felt when that tendril came in contact with her actually _mean_?

Even if it had been a… message, for lack of a better term… from Chaya, who was the 'he' that it had been referring to?


	25. Say You'll Share With Me

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This takes place a couple of weeks or so after the last chapter, at the same time as "Before I Sleep" occurred in canon; while the main events of that episode won't be happening here- John keeps the body of Elizabeth's future self somewhere a bit _less _easy to find than it was 'stored' in the show-, that's not to say there won't be some… interesting personal moments (On that topic, I hope the pot scene works out OK; I had a little trouble getting an idea for how John could give Elizabeth something when he's 'stuck' in Atlantis, but I think what I came up with works)

The Phantom of Atlantis

A couple of weeks later, with all offworld team members currently working on their own projects- Colonel Sumner, Lieutenant Ford and Teyla were carrying out surveys of some of the outer areas of the city while Doctor McKay led the science department in trying to crack the password that prevented them from re-dialling Earth-, Elizabeth stood reflectively on the balcony that had been unofficially designated as 'her' balcony- the balcony where she went whenever she wanted to think about recent events without anybody else bothering her-, her mind once again drawn to the central issues that had been plaguing her thoughts since Chaya's departure.

To this date, none of them had any clear idea about why she decided to depart like she had without providing them with any kind of explanation. It wasn't that Elizabeth felt they were _entitled _to the information, of course- she fully respected Chaya's right to not tell them things that she might want to keep private for some reason or another, particularly since she didn't seem to have any hostile intentions towards Atlantis-, but after leaving them so abruptly, she would have expected Chaya to at least explain her reasons out of politeness if nothing else. They'd attempted to dial Proculus again after Chaya had left, but their subsequent attempts to establish a wormhole had met with nothing but failure, the seventh chevron simply failing to engage; either the Stargate at the other end had been destroyed or Chaya had somehow prevented them from gaining access.

Although she hadn't voiced her opinion on that particular topic, Elizabeth was generally inclining towards the second opinion. She somehow doubted that Chaya would destroy the Stargate now after leaving it alone for all these centuries simply because they knew she was there, but preventing them from accessing the Stargate certainly fit what she knew of Chaya's personality; she wouldn't be surprised to know that the Ascended woman knew that Sumner wanted to question her for any further information she might have about the Phantom and had decided to avoid any possible confrontation in the easiest possible manner. Elizabeth freely acknowledged that Sumner couldn't actually do anything to _make _Chaya answer his questions, but that didn't mean that Chaya would want to have to put up with his questions anyway; preventing them from dialling the Stargate had probably seemed like the simplest option to avoid an uncomfortable situation.

She just…

Elizabeth sighed.

As much as the question of Chaya's motives and purpose remained a central issue, the one thing that Elizabeth _really _wished that she knew the answer to was what Chaya had meant by that last… comment she'd 'made' before she departed.

She had her theories, of course- given who Chaya had come to Atlantis to meet, coupled with the fact that she hadn't met many of the expedition during her stay in the city, there weren't that many people she could be referring to-, but with barely any actual _evidence _to base those theories on she was reluctant to actually voice them.

Besides, even if she _was _right- and she had her doubts that she was; why would… _he_… be interested in a _diplomat _in a city full of soldiers?-, why should it concern her? She barely knew the man, what she did know demonstrated that he was clearly a violent individual, he had displayed little real interest in getting to know her personally, he'd barely spoken to her beyond what was necessary for him to say in order to fill her in on the current crisis…

And yet, at the same time, he'd given her an Ancient shield device when he didn't have to, he'd told her his _name _(And it _was _his real name; she was sure of that if nothing else) when he didn't have to, he'd spoken to her for permission when attempting something as potentially dangerous as detonating a naquadah generator…

Even at his most brutal, when he'd killed the Genii soldiers who'd invaded Atlantis, the fact remained that he had _killed _them; if he'd genuinely been interested in violence simply for the sake of violence, wouldn't he have left them alive to 'prolong their suffering'…?

Why was it so _important _to her that the Phantom should turn out to be a good person?

As much as his actions had helped them to survive so far, she knew that Sumner had a valid point when he said that the Phantom's fundamental motives were still a mystery to them; there was always the possibility that he had some underlying motive for remaining hidden that none of them could guess at…

Elizabeth _knew _that there was a chance Sumner's suspicions were valid.

She was a trained diplomat; she knew that it was foolish to go into any situation and form an opinion of the people involved without first becoming aware of _everything _about the current crisis.

So why, even when she knew so little about the Phantom's own motives or background- given his surprisingly Earth-like name, even the _galaxy _he was born in was currently a mystery to her; 'John' didn't sound like a name from the Pegasus Galaxy but she had no idea how someone could have made it to Atlantis from Earth without using the Stargate-, did she spend her free time trying to figure out how his motives could be for the best without even_ considering _the idea that he might have malicious intentions for longer than a few minutes? She might pride herself on being a good judge of character, but she'd only met the man once in person, and even then the meeting had only lasted for a few minutes at most; what made her so _certain _that-?

"Penny for your thoughts?" a voice said from behind her.

Elizabeth nearly jumped in shock at the sound of the voice.

"_John_?" she said, turning around to look at the masked man standing before her in surprise, his long black cloak draped around him as he stared nonchalantly at her. "How did you-?"

"Get here without being seen by the colonel's security teams?" John finished for her, a slight smile visible on the left side of his face, the right still hidden under the mask that now gleamed in the sunlight. "I know my way around the city fairly well; working out a path here that allows me to avoid being seen by them isn't as hard as you might think."

"Ah," Elizabeth said, nodding slightly at that before she decided to ask another, hopefully neutral question.

"And… you're sure you're safe _being _here?" she asked, looking pointedly at him. She knew that it could be taken as a threat on her part- implying that she might contact Colonel Sumner to let him know where the Phantom was currently located-, but given how he'd interacted with her so far she had hopes that he would simply interpret it the way she'd meant it; a simple question hoping for an answer that would explain why he trusted her as much as he seemed to.

"Well, if you'd wanted to let Sumner and his men catch me, I somehow doubt I'd be standing here right now; you haven't exactly gone out of your way to make it _easy _for them to find me so far," John pointed out, a slightly teasing tone in his voice that would have angered Elizabeth if anyone else had used it but somehow seemed… different… when it came from John. "Besides, the door's locked and the glass is currently opaque; nobody can come here or see who _is _here without your consent-"

"Hold on; the glass is opaque?" Elizabeth repeated, turning to look in surprise at the glass that she could have _sworn _had been transparent- albeit coloured- earlier, only to see that John was right.

It _was _opaque now…

But Elizabeth could have _sworn_-

"Just a little privacy feature the Ancients included; it wasn't like they wanted people to be able to see them if some of them decided they wanted to try something… different… out here, so those with the Ancient gene can change the glass to be a bit harder to see through if they wanted to be left alone," John said, smiling slightly at the incredulous expression on Elizabeth's face as he broke into her train of thought. "Advanced civilisation or not, they were still _people_ when they lived here, you know; the fact that they ascended to a point where they don't actually _have _bodies any more doesn't mean they didn't have… urges…"

"Yes, I'm aware of that; someone back on Earth once had an… encounter… with an Ascended being that made _that _fact perfectly clear," Elizabeth said, cutting John off before he could go any further- there were some things that she did _not _want to think too much about, even with several thousand years between the events John was… hinting at… and the present- before she looked directly at him once again; evidently he wasn't going to clarify why he trusted that she wouldn't betray him any time soon. "Anyway, enough about the Ancients'… private lives; why are you _here_, anyway?"

"Oh, _that's _simple enough," John said, as he reached into his cloak with one hand before pulling it back out. "Happy birthday."

Elizabeth could only blink in surprise at the gesture, uncertain whether to feel touched or uncomfortable at the fact that John had risked being captured by Sumner's team just to give her a birthday present.

Then she realised just what he had given her, and her confusion only increased.

"A pot?" she said, looking back at John inquiringly.

She appreciated the gesture, but after the Ancient shield device he'd given her barely a week or so after she'd arrived in the city, a pot seemed like a pretty significant… change between types of gift.

"Given that it's hard to top an Ancient shield device in terms of something practical, I decided to just go for something nice visually and hope for the best," John said, shrugging nonchalantly as he looked at her. "I picked up a few things over my time in this galaxy- some little trinkets here and there to serve as mementos of the worlds I'd saved, that kind of thing-, and I found a few places around the city to keep them safe; I heard someone mention that your birthday was coming up, and I figured that…"

He shrugged. "Well, I thought you might like it; it's just a little thing, I know, but-"

"It's fine," Elizabeth said, raising a hand to cut John off before he could say any more, smiling slightly at the pot she now held in her hands before she looked back up at him. "It was… well, I appreciate the thought, John; thank you."

For a moment, John simply stood there, apparently uncertain about what he should do next, only for him to finally smile as he looked at her, the warm grin only partly visible but no less touching underneath his mask.

If Elizabeth had needed further evidence to assure her that John meant the expedition no harm, the look on his face right now was it; nobody that touched at somebody's appreciation of a simple pot as a gift could have plans against people they'd been trying to protect for the last few months…

And why was proving him trustworthy still so _important _to her?

"You're… welcome," John said at last, his tone suggesting that he was unfamiliar with that word passing his lips. Elizabeth couldn't help but wonder what could have happened to him in his past to make him uncomfortable with accepting praise- was he simply unused to staying around after he'd saved people from the Wraith in the past or was it something deeper than that?-, but shook that thought off; it wouldn't do her any good to think of questions that she couldn't learn the answer to at this point.

"Any chance I can return the favour at some point?" she asked, smiling slightly at him as she tried to change the conversation's direction to a more casual topic, only for the smile to fade as she saw John looking uncomfortably at her all over again.

"Uh… that's… really _not _practical; I… well, I lost track of dates a long time ago," John replied, looking apologetically at her, his discomfort at this topic easily visible even with his mask concealing most of his face. "I mean, I know how _old _I am in terms of years- mid to late thirties, really-, but I don't know the precise date or anything; I only even know it's your _birthday _because I heard someone mention that it was your birthday in a couple of days in a corridor a while back-"

"You 'overheard' someone in a corridor?" Elizabeth repeated, looking at John with what she knew was a slight trace of scepticism. As much as she might trust that he wouldn't betray Atlantis- after all the effort he'd gone to in order to protect the city for them when he could have just as easily driven them out, she was more than slightly convinced that he wasn't an enemy-, at the same time she couldn't help but be concerned about his ability to find out little things like that just by listening in on conversations.

If _he _could learn things like that about them just by listening in. what if someone- or some_thing_- else managed to gain access to the city and do the same…?

"Don't worry; I'm the only person who knows where to go to hear that kind of stuff, I assure you," John said, raising a hand to cut off the question before she could even ask it. "In any case, it took me _ages _to find some of my old routes, and that was when I had the city to myself and nothing but time on my hands while I was training; the odds of anyone finding the routes in an occupied city like this with no idea where to _start _looking and security teams all over the place are _pretty _slim, I assure you."

"You're… sure about that?" Elizabeth asked, looking uncertainly at the cloaked figure before her.

"Look, trust me on this; these access routes are _not _easy to find even if you know what you're looking for, and the only reason I even _started _looking for them in the first place was because I had a hunch there might be something there," John said, smiling reassuringly at her. "There's no _way _that the passages I use can be found by just _anybody_, I assure you; you'd need to actually know where to look if you were going to find anything that could do you some good, and even then the odds of you actually figuring out where to go once you were in there without any prior knowledge of how they're laid out are slim to none-"

"Passages?" Elizabeth said, raising a hand to look inquiringly at the man before her. "What 'passages' are you talking about?"

For a moment John simply stared back at her, an expression in his eyes that gave the impression he was suddenly trying to come to a decision on the spur of the moment, before he finally seemed to come to a decision.

"It's… connected to the way I… get around Atlantis," he said at last, looking uncomfortably at her. "A few passages here and there that aren't covered by the city's sensors; how I found them is a bit of a complicated story and I'd rather not get into it right now…"

For a moment Elizabeth thought about asking for more information- as the leader of Atlantis, she had a right to know about anything that might affect the city's security-, but she stopped herself before she actually said anything.

After all the time she'd spent telling Sumner that there might be a valid reason for the Phantom not telling them everything he knew about the city straight away, it would be almost hypocritical of her to insist that John tell _her _something if he didn't want to talk about it simply because _she _thought he should tell her. John had already assured her that nobody else knew of or could use the tunnels apart from him, and given how long he'd been here, she had little reason to assume that he was lying.

Besides, when you got down to it, Atlantis was John's city more than it was theirs; as he'd implied during his initial conversation with Kolya, if John didn't _want _them in the city, they'd probably have been driven out long ago. If he hadn't attempted anything by now- to say nothing of how much effort he'd gone to stop the nanite virus from spreading a few weeks ago; if he'd wanted to get rid of the expedition why would he have gone to so much trouble to protect them from something that could have lowered their population to a level that he could have defeated more easily?- he probably wasn't going to do so; John having access to some secret passages didn't change that fact that much.

If anything, the fact that he knew about Atlantis's secret passages and hadn't yet used them against the expedition only confirmed for Elizabeth that she wasn't wrong in trusting him; if nobody else knew about these routes, he could have easily faked an 'accident' for Sumner or some of the military personnel who'd been causing him difficulty so far, and yet he'd done nothing of the sort.

"Don't worry about it," she said at last, looking reassuringly at John as he stared uncomfortably at her; clearly he hadn't know how she was going to react to his statement. "I… well, as crazy as Sumner might see it as, I trust you."

It was hard to be sure with the shadows caused by the mask, but Elizabeth could have sworn that John's eyes widened at that last comment.

"Really?" he said, looking at her with a tone of barely-disguised surprise. "You don't… well, you don't want to know about the passages? I mean, Sumner'd probably be _really _eager to block some of the entrances up to limit my access to the city…"

"Well, the way I see it, if you'd been going to use your knowledge of the city against us you would have done it already," Elizabeth said, smiling reassuringly at him to take any potential sting out of her words. "Given the lengths you've gone to in order to protect the rest of my expedition so far, the fact that you know something else about this city that we don't doesn't change the fact that you've been nothing but helpful for us to date; if you don't want to tell me something about the city…"

She shrugged. "You've been here since before any of us; if you think it's not time to tell us about something, I'm hardly in a position to demand answers.

For a moment, Elizabeth and John simply exchanged silent smiles- Elizabeth couldn't help but wonder if John felt that same… _stirring_… in her chest as she did when she saw the half-smile under his mask-, only for the moment to be broken when Elizabeth's radio activated.

"_Doctor Weir_?" Doctor Grodin's voice said over her radio. "_Doctor McKay just called; he wants to talk with you and Colonel Sumner about something he found in the Ancient database_."

"On my way," Elizabeth confirmed, tapping her earpiece briefly to respond before she turned back to look at John. "Sorry, John; duty-"

"Calls, right?" John replied, nodding in understanding. "Don't worry; just make sure you get that pot somewhere safe. I'll… well, I'll be around for when you next need me, huh?"

"I wouldn't have it any other way," Elizabeth replied, a slight smile on her face as she nodded back at John as she placed the pot in her right hand and lowered her right arm down to the side; so long as she was careful and went directly to her office- she could easily claim that she wanted to check something out before she met with McKay-, she should manage to find a secure place to store the pot in her office while she attended her next meeting without anybody seeing the pot itself.

It might be paranoid, but she had a feeling that Sumner would even regard a _pot _from the Phantom as a potential trap…

It was only when she took in the glass window before her that Elizabeth realised that it had suddenly turned clear again; a quick glance behind her swiftly confirmed that John had vanished while she was moving the pot to her right hand, leaving no trace that he had ever been present.

Even knowing that she could trust him, Elizabeth couldn't stop herself from shivering slightly.

The _speed _that John must have to be able to vanish from view on an open balcony that rapidly, to say nothing of the depth of his knowledge of the city if he was able to arrive and leave what seemed like any location he wanted that rapidly…

The more she learnt about the man known to the Pegasus Galaxy as the Phantom of the Ancestors, the more grateful Elizabeth Weir became that what she learned also leant increased weight to the idea that he was on their side.

She just wished she could identify _why _she felt so… _strange_… whenever she thought about him; what _was _it about that man that interested her so much…?

* * *

AN 2: I'm not _entirely _happy with this chapter, but we get on to more straightforward territory next up; just consider this a 'filler' before the main events


	26. It Feels Like We're Running Out of Time

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: As with last chapter, the events of this one take place around the time of an episode of the series- "The Brotherhood" in this case-, but with some _significant _changes from canon events due to the Phantom's actions…

The Phantom of Atlantis

As she sat in her office looking over the latest reports of the various teams, Elizabeth allowed herself a brief sigh of relief at how much lighter their workload had become these past few weeks.

Ever since Chaya's departure from Atlantis, even if the mystery of her presence and her long-term motives remained, the offworld teams had encountered little to no real danger in their travels. They'd managed to establish a few trading agreements for further food supplies, they'd discovered a few sites that might make a useful place to evacuate to, and even McKay's continued research on the code that prevented them from shutting down the shield when dialling the Milky Way was making some progress. The shield was still activating whenever they tried to dial their original home galaxy despite McKay's best efforts at cracking the code, but the Canadian scientist remained confident that they'd have something worked out soon; he continued to assure Elizabeth that he just needed a little more time before he found what he was looking for and the problem was solved.

Privately, Elizabeth was beginning to wonder if McKay wasn't as far on with that particular line of research as he thought (Or _claimed _to think at any rate); even Zelenka's research team had recently discovered Atlantis's deep space sensors- admittedly, 'recently' translated into 'the last couple of hours' and she was still the only person outside Zelenka's staff who knew about it, but the fact remained that they'd made a discovery without McKay-, while McKay's own research team hadn't made any kind of significant discovery since their examination of the Ancient satellite and the crashed Wraith cruiser (Which, unfortunately, had been too badly damaged and decayed to provide them with any indication of a weakness they could exploit in future confrontations).

With that in mind, McKay's continued eagerness to go off on any missions that might arise had left her wondering if the scientist was trying to find a convenient excuse for not having actually accomplished anything yet by giving himself too much to do; whether he actually consciously thought about this or it was primarily a subconscious action on his part was something she didn't know, but she retained her suspicions.

Then again, the recent missions _had _been for a rather important purpose, so she supposed that she had little real right to be suspicious of him; he was, after all, their greatest available expert on Ancient technology, so it was really only natural for him to be involved in these particular missions. Shortly after her last encounter with the Phantom- which nobody knew anything about; she'd managed to smuggle the pot he'd given her back to her room and subsequently left it in a safe place in one of the cupboards she used to store her clothes-, McKay had managed to find a few addresses that seemed to indicate the location of Ancient research outposts which seemed likely to retain their ZPMs.

Colonel Sumner's team had been over most of them to see what they could find, but so far there'd been no luck; either the outposts analysed had been totally free of ZPMs or what ZPMs were there had completely run out of power a long time ago. Their current destination- a planet with a low-level civilisation apparently equal to Earth in the middle ages- was the last address on the list, but so far Elizabeth had yet to hear back from the team; the last news she'd heard was a message from Colonel Sumner that they were trying to convince the natives that they had come from Atlantis, and that had been several hours ago-

"Incoming wormhole!" Doctor Grodin's voice suddenly yelled at her from off to the side, breaking into her train of thought as she stood up and rapidly walked towards the control room.

"Who is it?" she asked, looking curiously at the young man currently sitting at the Atlantis DHD.

"It's Colonel Sumner's team," Doctor Grodin replied, glancing back at her.

"Lower the shield," Elizabeth said, nodding briefly at him before she turned to leave the control room, walking down the stairs to stand in front of the Stargate as Sumner's team came through the wormhole.

It didn't take Elizabeth long to note the conspicuous absence of a ZPM from their hands; evidently, this search had proven just as fruitless as the others.

"How did it go?" she asked, deciding to stick to the obvious question first; she could hear how it had actually gone in more detail once they were in the conference.

"Oh, just peachy; the people just wanted to understand why we'd come back to get something _we already took_!" McKay said, looking over at Elizabeth in frustration before Sumner could answer the question himself.

Elizabeth blinked.

"Excuse me?" she said in confusion.

"Apparently the ZPM that was kept on that planet was claimed around a decade ago," Teyla explained, stepping forward to take up the story from the clearly annoyed scientist. "It is an interesting story, but I feel we should wait to discuss it for when we are in the conference room."

"Agreed," Elizabeth said, as she indicated the stairs behind her that led up to the conference room. "Have Beckett check you out and then meet me up in the conference room."

The subsequent medical check-up fortunately didn't take long- given the lack of Goa'uld in this galaxy the Atlantis expedition were generally able to forego the MRIs that remained standard SGC protocol, although the tradition check-over for viruses could still take some time-, but even still, Elizabeth was unable to stop herself from impatiently tapping her fingers while she waited; one of the things that she had appreciated about her old job as a diplomat was that things generally operated on a precise schedule, which wasn't something she had the chance to experience that often in her current situation. Finally, Atlantis's main offworld team came into the room and sat down around the table,

"So," Elizabeth said, as she looked around at the four people sitting opposite her, "what actually happened to the ZPM?"

"According to the legends that we were able to translate from the Sudarians, which we subsequently confirmed after we looked over their archives," Teyla began- evidently she had been the main person to gather this information, given her unofficial role as the team's diplomat-, "an Ancient came to Dagan through the Stargate from Atlantis, entrusting them with a rare treasure which they referred to as the "potentia", and whose depictions match that of the ZPMs. This Atlantian told them to keep it hidden from the Wraith at all costs, which they claim to have done until almost a decade ago."

"And… what happened to it a decade ago?" Elizabeth asked, looking inquiringly at the Athosian woman.

"What else?" Sumner said, his expression grim as he looked up at Elizabeth. "The Phantom came to the planet, proclaimed himself to be the 'spirit of the Ancestors', passed their 'tests' to find where the damn thing was being kept, walked away with the ZPM, and hasn't been seen since-"

"Which," McKay added, raising a finger as he looked at Elizabeth, his expression appearing particularly annoyed, "suggests that the Phantom- wherever he is- has access to _more _ZedPMs than the one we found powering the city when we got here!"

Elizabeth could only stare at McKay in confusion.

"And you've come to that conclusion because…?" she asked uncertainly; she really couldn't see how this latest turn of events could translate into McKay concluding that the Phantom had access to multiple ZPMs.

"Look, the people we just visited regarded the ZedPM as a holy relic," McKay explained, looking pointedly at Elizabeth as he continued. "Given that they'd never have used it as a power source, and it's unlikely the Ancients would have left an even _partially _depleted ZedPM with a society like that for safe keeping- why go to that much effort to protect something that _isn't _able to provide full power?-, it seems like pretty good odds to me that the ZedPM the Phantom recovered from _there _would have been at least almost fully charged when he took it away. Assuming that the ZedPM he acquired from there is the same one as the one we found in the city when we got here, it should still have had around _seventy_ percent power available to it in a worst-case-scenario; all it would have needed to do was keep the force field active to prevent the water from getting in and provide enough lights and atmosphere for _one man _to live in this city in relative comfort-"

"Hold on a minute, let me see if I've got this right; you're saying… if the ZPM that we're using now had come from _there_, it should have more power available to it than it actually does?" Ford asked, looking at McKay for clarification.

"Unless this 'Phantom' guy's more of an idiot than we give him credit for and did something stupidly power-draining in between getting the ZedPM and our own arrival- and, given what we've seen of his ability to survive so far, I'm pretty sure he's _not_ that stupid-, that's it exactly," McKay said, nodding in confirmation at the young lieutenant.

"So… what are you saying?" Elizabeth asked, waving a hand promptingly at McKay. "That there are more ZPMs around here than the one we're using?"

No sooner had McKay opened his mouth to reply than he paused, his expression briefly lost in thought as he considered what Elizabeth had said, before he finally shook his head.

"Actually… I don't think there _are_," he said, his voice slow as he spoke, as though he was putting a great deal of thought into what he was saying as he said it. "I mean, as I already said, the Phantom isn't stupid, and storing a large bunch of ZPMs in something as important as Atlantis would definitely qualify as being _pretty _stupid in my book…"

"Keeping regular access to the very things that he needs to provide this city with the ability to defend itself is _stupid_?" Sumner asked, looking critically at McKay as though wondering if the scientist had lost the plot at some point.

"OK, I grant you that it seems like a good idea on paper, but what if the Wraith had ever made it into the city?" McKay pointed out as he looked back at Sumner, his expression giving no hint of the indignation he must have felt at the implication of the colonel's statement. "One lucky shot- well, one _stupid _shot; anyone trying it deliberately would have to be idiotic or suicidal- in the wrong place as they're running around here, and the Wraith could blow up the ZPMs and trigger an explosion that could wipe out at _least _a decent-sized chunk of this planet! _We _might be able to set up a secure location to protect them in the city, but the Phantom's one guy with limited resources; I don't care _how _good he is, there's no way he could have been _sure _of sticking multiple ZedPMs somewhere where the Wraith couldn't be _guaranteed _not to shoot them by accident!"

For a moment there was silence around the conference table as the team contemplated what McKay had said, before Ford finally broke it with an uncertain nod.

"You gotta admit, that _does _make sense," he said, nodding slightly as he exchanged glances with the rest of his team. "I mean, I heard of a couple of reports when I was still at the SGC about the science teams saying that one ZPM could be capable of maybe blowing up a planet if it was damaged; if there were a lot of 'em in one place…"

"Particularly when that 'one place' is somewhere that would be as significant a target as Atlantis; no matter how many precautions the Phantom might have made to try and keep the Wraith from getting here, he's only one person who can't be everywhere at once," McKay added, nodding resolutely as he glanced around the table. "He must have some secure offworld location where he can keep any extra ZedPMs he might have acquired; if he's acquired the two that we know of- the one from Dagan and the one we're using at the moment-, it only makes sense that he's got a few more hanging around somewhere where he can get to them at short notice."

"In other words, there might be multiple ZPMs on some offworld location that we haven't visited yet?" Sumner asked, looking pointedly over at McKay.

"Well, assuming we're correct about this-" McKay began.

"Beginning with the idea that you _are _correct," Sumner interjected, his gaze intensifying as he stared at McKay, "how would you recommend we go about finding them?"

McKay had just opened his mouth to speak when Zelenka suddenly hurried into the control room, looking anxiously over at Elizabeth.

"Sorry to interrupt," he said, looking apologetically around at the assorted members of the team before his gaze re-settled on Elizabeth, "but we have a problem."

"What is it?" Elizabeth asked, looking back at the Czech scientist.

"I've just managed to complete linking our computers to the Atlantean long-range sensors-" Zelenka began.

"Hold on; we have long-range sensors?" McKay repeated, turning to look critically at Zelenka. "I didn't know we had long-range sensors; why didn't anybody _tell _me that we had long-range sensors?"

"Nobody knew until recently," Zelenka replied, shrugging apologetically at McKay. "As far as I could tell, they've been running silently in background along with our other primary systems; they only recently jumped to the foreground."

"Why would that happen?" Sumner asked, his own interest heightened by anything relating to Atlantis's security (Elizabeth just hoped that he wasn't going to accuse the Phantom of having limited their access to the city; personally she considered it more likely that, given Atlantis's currently limited power supply, the city had just been keeping the sensors on low power until they detected something important).

"Well, I _think _it might be because of the unidentified craft about the size of a Wraith dart heading for us," Zelenka finished, looking over at Sumner with a slight glare.

"_What_?" Elizabeth said, as she and the rest of the team stood up and hurried for the control room, Zelenka leading the way as he showed them to a laptop that he'd connected up to one of the Ancient control consoles.

"I'm sorry," he said, as he sat down in front of the screen that was currently displaying a blurred picture that certainly looked like a Wraith dart. "The sensors picked it up days ago but its taken me until now to finally decipher what they've been trying to tell us-"

"And you never thought to ask for _my _help?" McKay asked, glaring over at Zelenka.

"You were always busy," Zelenka replied with a dismissive shrug before he turned his attention back to the screen. "I still don't know _how _this happened; my best guess is that it used neighbouring Stargate to fly towards us at maximum speed ever since the Wraith discovered we were here-"

"We can worry about the _how _of it later; right now we have to stop it," Sumner said, glaring resolutely at Zelenka. "How far away is it?"

"Approximately… twenty-seven minutes," Zelenka replied, glancing briefly at the laptop before he turned back to look at the others.

"Right," Sumner said, nodding briefly as he looked over at McKay. "Doctor McKay, get the gateship pilots together; we need to get in the air as soon as-"

"Someone's already doing it!" Grodin suddenly yelled from his seat at another control console.

"_What_?" Sumner yelled, spinning around to look at the other man.

"According to these readings, a gateship just left via the roof-hatch and is taking a direct intercept course towards the oncoming dart," Grodin replied. "I've no idea who could be piloting it, but-"

"Seems simple enough to find out; just look at who you told about these sensor readings _before _Doctor Zelenka told us," Sumner, said, glaring briefly at Grodin before turning to look at the Czech scientist. "Doctor, I thought I'd made the situation clear; I _cannot _be left out of the loop-!"

"Colonel Sumner, I hadn't even told anyone else _here _about what the sensors were telling me before I told you; how could anyone _here _have given the order?" Zelenka interjected, looking over at the colonel with a clearly confused expression. "Whoever is behind this, they have somehow become aware of the presence of the dart _without _any of us needing to tell them ourselves, and since I can assure you that nobody has left this room since I determined what we had discovered, I have no idea who could have alerted anyone else to this latest turn of events."

"Well, _someone _had to-" Sumner began.

"_Atlantis control room_?" a voice suddenly said over the main radio, a voice that Elizabeth recognised instantly even as she fought to control her reaction, "_this is the Phantom of Atlantis; I am in the… gateship… that just departed the main bay, moving to intercept the oncoming dart_."

For a moment, there was nothing but stunned silence inside the control room, everyone who had heard the message staring is shock at the thought that the man they'd been searching for since their arrival over a year ago was just… _talking _to them like this… before he spoke again. "_Just thought you should know_."

After another brief, stunned silence- Elizabeth didn't trust herself to speak; after the privacy of their last two conversations the possibility that she'd slip up and say something that would give away the fact that she'd spoken to 'the Phantom' before now was too great-, Sumner stepped forward and activated the radio,

"What the _hell _do you think you're doing?" he yelled over the radio; Elizabeth briefly wondered if she should try and arrange for the rest of the people in the control room to leave, but swiftly decided that it wouldn't be worth the effort. "My pilots can _handle _this-"

"_From what I recall from your mission reports, your pilots' combat training with these things is limited to your attempted rescue of the Athosians after you arrived here and that brief scuffle over Chaya's planet- where, I might add, your weapons were disabled so that you _couldn't _shoot back_," the Phantom countered (Elizabeth could almost picture the surprisingly 'familiar'- for all that she hadn't seen it that often- teasing smile on his face underneath the mask before she forced her attention back to the current issue). "_Given the time it would take you to rally your available pilots and the rate at which the dart is approaching, your men would probably end up having to fight the dart around Atlantis's towers; I'm currently your best chance at taking this thing out of the picture before it gets too close. You can either complain about me doing what I had to do to protect the city, or you can let me do what I came here to do and take out this dart; clear_?"

Once again, silence dominated the control room, all eyes fixed on Colonel Sumner as he stared out of the nearest window overlooking the sea; if Elizabeth understood the sensor readings correctly, Sumner was currently looking in approximately the direction from which the dart was approaching them, which meant that the gateship that currently held the Phantom would be somewhere in that area as well.

Finally, after a brief moment where Elizabeth noticed Sumner clenching his fists like he wanted to punch something, he turned back to the radio.

"_Fine_," he said simply, his tone direct and his expression cold as he glared at the radio. "Just… do what you have to do and get back here, all right?"

"_Where else would I go_?" the Phantom replied, once again sounding like he was smiling slightly before he spoke again, his tone once again serious. "_I'll be back soon; in the meantime, just keep an eye on the sensors and prepare to defend yourselves if this sucker gets past me_."

Before Sumner could say anything else, the radio signal was terminated, leaving the Atlantis senior staff looking uncertainly at each other before Grodin broke the silence.

"Uh… according to the long-range sensors, the Phantom's gateship will be within firing range of the Wraith dart within the next ten or so minutes," he said, as he looked uncertainly at the others. "Shall I continue tracking?"

"Do what you can," Sumner said, nodding briefly at Grodin before he glanced over at McKay. "Doctor McKay, how soon can we get the control chair up and running?"

"Well, theoretically all it needs is someone to sit in it-" McKay began.

"Good; that'll be your job right now," Sumner said, nodding briefly at the scientist before he turned to look at Lieutenant Ford. "Lieutenant, gather the security teams together and direct them to the gateship bay; have half the team remain inside the main bay and have the other half take cloaked ships out of the tower-"

"Hold on; are you planning on trying to capture him _again_?" Elizabeth cut in, glaring at Sumner as she stepped forward to stand in front of him. "Colonel, as much as I respect your authority in military matters, the Phantom is currently trying to _help_ us-"

"By dealing with a situation that he appears to have known about long before _we_ did?" Sumner countered, returning Elizabeth's glare with one of his own. "If the Phantom genuinely wished to help us, he should have contacted us once he knew about the dart-"

"From what I've heard about their size, one Wraith dart is hardly a serious danger to this city," Elizabeth interjected, her arms folded as she glared back at Sumner. "Given our current lack of any ships other than the gateships, alerting us to the dart's existence earlier would have accomplished nothing, and in any case we have no way of knowing just how _much _in advance the Phantom was alerted to the dart's presence in this system; he might have simply learned about it when the long-range sensors activated and been quicker to understand what he was looking at than we did-"

"If he was genuinely concerned with helping this city, why wouldn't he simply alert _us _to the dart's existence rather than take action himself?" Sumner said, his arms folded as he looked critically back at Elizabeth. "Doctor Weir, your diplomatic ability to see both sides of the situation is commendable, but we are presently dealing with a military situation where an unknown combatant has concealed potentially vital information for unknown purposes; given this situation, apprehending him to determine the scale of his knowledge of the city can only be beneficial in the long term-"

"The dart has been destroyed," Grodin said, his voice cutting through the potentially-heated argument between the two leaders of Atlantis as he turned to look at them.

"_What_?" Sumner said, spinning around to stare incredulously at the British scientist, his argument with Elizabeth at least momentarily forgotten in his shock at this latest turn of events. "I thought you said that he'd take ten _minutes _to get within firing range of the dart-"

"That's what I thought based on our previous knowledge of how the gateships operated," Grodin confirmed, looking apologetically back at Sumner. "However, it would appear that the Phantom managed to accelerate his ship's speed via some unknown method; given that he took his jumper from the hanger directly above us he cannot have simply been using a modified ship or we would have already identified it as such. My best guess is that he accelerated the gateship's speed by using its drone weapons to provide additional thrust without triggering them to fire by accident; it would be difficult to maintain that degree of control over something that was fundamentally designed to serve as a weapon rather than as a means of propulsion, but it _is _theoretically possible."

For a moment Sumner looked like he was about to start berating Grodin for this latest mistake, but he stopped himself before he could say anything else, evidently acknowledging that he couldn't get angry about something that nobody could have predicted would happen.

"_Fine_," he sighed, his tone demonstrating his exasperation at this latest turn of events even as he turned to look at Ford, who was still standing off to the side; after Elizabeth and Sumner had begun their brief 'argument' Ford had apparently decided that it would be best if he just waited until they came to a decision about this either way. "Ford-"

"_Attention Atlantis_," the Phantom's voice said over the radio, cutting the colonel short mid-sentence once again. "_This is the Phantom; the dart has been destroyed and I'm returning to the city. You might want to boost the long-range sensors to maximum power and trace back along the dart's flight-path; with what I know of Wraith tactics- coupled with the fact that darts are normally short-range fighters-, there's almost certainly _something _at the other end of that line that is going to be _nothing _but trouble for us_."

"'Us'?" Sumner repeated, pushing Grodin aside as he stepped forward to speak more directly into the radio. "There _is _no 'us'… whoever you are; you're a rogue element outside the hierarchy of this expedition-!"

"_I'm still a part of this city's defences, Colonel Sumner_," the Phantom replied, his tone a solemn one that Elizabeth hadn't heard since he'd told Kolya to release her or be shot. "_You don't have to like me; you just have to get used to me doing what needs to be done in desperate situations_."

"What 'needs to be done' is for you to-" Sumner began.

"_See you around_," the Phantom interjected, his tone casual as he terminated the radio connection, leaving Sumner staring with a mixture of criticism and shock at the console that controlled the radio.

"_Right_," he muttered, nodding resolutely as he glanced at his side; the team had been so quick to come to the briefing that they all still carried their weapons, his gaze quickly falling on the P-90 still hanging by Ford's side before he turned to look at Grodin. "Given what we _now _know about the gateship speeds, how long will it take the gateship to get back into the bay?"

"Uh… two or three minutes at most; why?" Grodin asked, looking at Sumner uncertainly.

"Just enough time, then…" Sumner said, half to himself, before he turned around to look at Ford. "Lieutenant, you're with me; we're going to the gateship bay."

"Yes sir," Ford said, nodding briefly at the colonel before the two of them began to run towards the gateship bay.

Elizabeth barely even hesitated; waving a brief hand at the rest of the people in the room to stop them from following her, she swiftly turned around and began to jog after Sumner and Ford as they hurried towards the gateship bay.

Elizabeth would be the first to admit that she wasn't sure what she expected to accomplish by this action. She could hardly object to Sumner trying to capture someone who'd just stolen a ship for his own ends; just because the Phantom _hadn't _done anything didn't mean he _couldn't _have done something with it, and the issue of his fundamentally unknown motives remained a concern no matter how certain she was from her own meetings with him (Which she'd promised not to mention, frustratingly enough) that John didn't mean them any harm…

In the end, however, the reason she was doing this was simple; she wanted to see John again.

She had no idea _why _she was going to these kind of lengths to see someone when the only thing she really _knew _about him as a person were his name and a vague idea of his age; all she knew was that she _had _to see him…

Then she, Colonel Sumner, and Lieutenant Ford ran into the gateship bay, only to see the gateship that had so recently destroyed a Wraith dart 'slotting' into the only currently-empty space in the bay after lowering itself back into the city following its entrance via the upper hatch, with no sign of a pilot in the cockpit window. Elizabeth briefly thought that she caught a glimpse of a long black cloak hurrying towards a corner of the bay, but by the time she glanced in the direction the cloak had been running it had apparently vanished, with no sign of movement in that part of the bay to give away where he had gone.

"What the _hell_…?" Sumner muttered, looking at the clearly empty gateship before him. "How does he keep _doing _that?"

Elizabeth had a theory- particularly given what John had told her during their last meeting about those 'passages' he used to get around Atlantis-, but she wasn't going to mention it; right now, capturing John wouldn't accomplish anything.

"_Doctor Weir_?" Zelenka's voice said over the radio, cutting Sumner off before he could voice any further opinions on their next course of action.

"Yes?" she said, hoping that, whatever Zelenka had to tell her would draw attention away from the current issue; the last thing she wanted was for Sumner to find one of John's passages and take away what was possibly the only thing keeping him out of a cell simply for trying to do the right thing without worrying about the proverbial red tape (And _why _did she keep trying to defend his actions to _herself_?).

"_You need to get down here as soon as possible_," the Czech scientist's voice said, clearly anxious at whatever he had just discovered. "_Doctor McKay and I found something that you should see_."

Exchanging a brief glance with Colonel Sumner- she was relieved to see that he at least seemed to be taking Zelenka's warning as seriously as she was; the Czech scientist might not be as skilled as McKay but he was a lot less prone to exaggeration that the Canadian was-, Elizabeth turned and walked out of the hanger bay, making her way as quickly as possible back to the control room, McKay and Zelenka standing around the control console for the long-range sensors with anxious expressions (Elizabeth briefly noted Teyla's absence, but swiftly decided it was nothing to be worried about; Teyla had probably simply concluded that she could contribute nothing further to this particular situation and gone to her quarters).

"What is it?" she asked, looking between the two scientists as Sumner and Ford walked into the room, taking up position to either side of her.

"Well, based on the Phantom's… suggestion… about finding where the dart had come from," McKay said- clearly he didn't want to think of the Phantom's comment as 'advice'; that would have implied he'd done something that McKay couldn't have done himself-, "we traced the dart's flight path back along its projected course, and what we found…"

He swallowed slightly, a clearly anxious expression on his face. "Well, it's a _definite _cause for alarm."

"What is it?" Sumner asked.

"This," Zelenka said, tapping a few buttons on the console in front of him and McKay. Instantly three large shapes appeared on the nearest screen, somehow sending a brief shiver down Elizabeth's spine even without a clearer image of whatever she was currently looking at.

"What are they?" Sumner asked, his arms folded as he looked critically between the scientists.

"Wraith hive ships," McKay said, looking grimly over at the colonel. "And, judging by their current speed, they'll be over Atlantis in just under two weeks."

If Elizabeth had been the type to swear, she would have done so at that point.

Two _weeks_? They'd barely even begun to examine Atlantis' offensive capabilities- with their only ZPM operating at barely fifteen percent power nobody had wanted to risk accessing the kind of power that such an important system would require to operate unless it was necessary-, what little they had examined suggested that it was low on drone weapons with little else available to use as firepower…

And now they had barely two _weeks _to get everything up and running to an extent that would allow them to go up against _three _fully-armed Wraith hive-ships?

_This is bad…_ Elizabeth reflected grimly to herself.

_This is very, _very _bad_.

* * *

Unknown to Elizabeth, even as she learned about this latest turn of events, the dark-clad figure who had so recently saved the city once again was currently crouched in his usual 'control room observation point'- as he thought of the part of the maintenance tunnels where he usually hid when he wanted to keep an eye on the situation in the control room-, silently listening to this latest turn of events.

_Three Wraith hive-ships in two weeks, and I can barely set _foot _in the main city without Sumner trying to lock me up in case I make a bad call_… he reflected, groaning slightly in frustration as he looked up at the ceiling just a few inches above him. _Great_…

There was no question about _what _the Wraith wanted, either; while Atlantis itself could be a valuable prize- even with the Ancient-gene-encoded technology, there were still several things in the city that the Wraith could salvage and use for their own ends-, what the Wraith _really _wanted right now was something that they could have only acquired from torturing Captain Gemmel before his death.

The Stargate address to Earth.

The address that could _only _be dialled from the Atlantis Stargate, and which he had protected from Wraith discovery the only way he could without preventing Elizabeth's team from being able to _get _here in the first place; by programming the shield to activate every time someone tried to dial an address in the Milky Way galaxy.

At the time, short of locking Earth out of the dialling computer- which he was pretty sure would have stopped anyone from Earth coming _here _as well-, it had been the only solution.

Right now, however, the Atlantis Expedition's only chance to fight off the Wraith hive-ships was to contact Earth and request assistance, which was something that they _couldn't _accomplish as long as that particular program was still active.

_In other words_, John reflected to himself, as he looked grimly out at the people who were faced with an attack on a scale that they could never have imagined they would be confronting when they first came to this city, _it's time for Elizabeth to receive the code_.

He just hoped that she could come up with a way to enter it into the system without attracting too much attention…

* * *

AN 2: If anyone objects to Zelenka finding where the dart came from this quickly when he said it would take him a couple of hours in the show, it should be noted that we don't actually _know _how long it took him to do the job- the 'couple of hours' thing was only an estimate; it might have been quicker-, he had McKay to help him here- the man might be a pain but he _is _good with Ancient tech-, and there's no way of knowing what John might have done with the computers over the years to make the sensors more sensitive to external input; just because he was unlikely to ever _need _them doesn't mean he'd have neglected them.


	27. How Could I Just Let You Walk Away?

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Timeline-wise, this takes place the night after the previous chapter, so they've just discovered the approaching Hive-ships and have agreed to discuss possible courses of action to take against the Wraith the next morning, spending the current night trying to _think _of the aforementioned plans

The Phantom of Atlantis

As she sat in her office that night, staring over files long after every other member of the expedition had gone to bed, Elizabeth wished that she could bring herself to focus more on the papers before her.

It was almost impossible to believe how much things had fallen apart in the last few hours since the Phantom had shot down that Wraith dart; with the discovery of no less than three Wraith hive-ships heading for them at a speed that left them little to no time to prepare any kind of defence, fear and anxiety was rapidly spreading throughout Atlantis, particularly given their continued lack of ability to contact Earth for reinforcements.

Reinforcements…

That was another thing Elizabeth didn't want to think too much about; their lack of any military-based allies in this galaxy. Their few truly successfully alliances with other cultures had all been based around nothing more than trades for food- commonly providing medical supplies and an offer of protection from future Wraith attacks in exchange-, but, as helpful as they'd been, none of those worlds had anything further to offer them than extra soldiers in the event of an attack. The only even remotely technologically advanced culture they'd discovered to date were the Genii- the Hoffans had inclined more towards biological research-, and even without the current tense relationship that existed between their two peoples the Genii didn't have much more to offer than some prototype nuclear weapons that weren't even fully developed yet.

Then, of course, there was the issue of Earth; no matter how much she tried to think of something else, in the end it always came down to their continued inability to send a message back to Earth. They'd tried to dial every safe Stargate address located in the Milky Way that they could think of- even resorting to some of the more uncertain ones in their desperation, such as the addresses for Chulak or that planet where SG-1's android duplicates had been created (She still couldn't quite remember the name of that one)-, but so far nothing had worked; the shield continued to activate and cut off radio transmission whenever the wormhole activated, 'snapping' into place before the unstable vortex could be expelled.

The science teams had done their best to shut it down, of course, but so far every attempt to crack the code that apparently controlled the shield had met with failure, and they still had a nearly limitless amount of possible words that could be used from the database. McKay had suggested trying to get rid of the shield by overloading it to prevent it from activating in the first place, but Elizabeth had quickly shot that down when the Canadian scientist had admitted that he wasn't certain if he'd be able to repair it afterwards; given their current inability to construct an Iris like the one used on the Earth Stargate, they would have been rendering themselves automatically vulnerable to invasion from the Stargate, and with so few advantages available to them already they were in no position to forsake something that potentially useful.

She just couldn't _believe _how frustrating it was; after spending the better part of the last year learning about the most incredible city the Ancients had ever created, exploring worlds and making contact with people like nothing Stargate Command had ever encountered back home (_such as the Phantom_, a traitorous part of her mind commented before she shoved that thought to the back of her mind; now was _not _the time to think about that!), they were going to have to run away and find some other planet to settle on, all because of a 'communication problem'…

"_Doctor Weir_?" a voice said over her radio, blinking Elizabeth out of her thoughts as soon as she registered the voice.

"John?" she said as she raised her hand to the radio, taking a brief glance out at the control room to make sure nobody was coming to talk to her; the current night shift only had a few technicians on duty rather than the larger number that would have occupied the room during the day, but it was still enough people that she wouldn't want to risk attracting attention to herself unless she had to do so. "What is it?"

"_Can you come to the balcony for a moment_?" John asked, his tone sounding slightly hurried; if Elizabeth didn't know John better she'd have almost assumed that he was scared of something. "_I have… well, there's something I need to give you_."

For a moment Elizabeth wasn't ashamed to admit that she hesitated- was she really going to voluntarily go for a meeting with a man when she only knew the basics about his past and his motives?-, but she swiftly pushed any such doubts aside; after everything that John had done for the city since they'd arrived, even if he hadn't proven himself completely to Colonel Sumner, he'd proven himself to _her_ as far as she was concerned.

If he had something else planned…

_Well_, Elizabeth mused, as she reached into her pocket to make sure that the Ancient shield device John had given her so many months ago remained there, _that's what this is for_.

She might not _like _having to think of John as a potential enemy, but she had to at least _try _and maintain a detached attitude towards him if she was going to be a professional leader for the city…

She just wished that _doing _that was as easy as _thinking _it.

Shaking such thoughts out of her mind as she walked through the control room- briefly making a comment about needing some fresh air as she passed by the night staff- one of the advantages of being in command; nobody questioned some of the little things she did so long as she did nothing _too _unusual- before she walked out onto the balcony, closing the door behind her as she did so. She had barely been standing there for a few moments, looking up at the differently-starred sky with a silently reflective expression, before she heard a slight 'thump' behind her and knew that her 'guest' had arrived; he must have needed to make a slight jump from however he got around Atlantis to land on the balcony itself.

"You're here, then?" she said, turning to look at John with a slight smile, his long black cloak, as always, serving to conceal most of his body as he stood before her.

"Did you have any doubt I wouldn't be?" John countered, smiling slightly at her under his now-familiar mask as he walked up to stand beside her, before his expression became grimmer as he stared at her. "Particularly not with this _latest _turn of events…"

"The hive-ships?" Elizabeth asked, looking at the man now standing beside her for clarification.

"Precisely," John said, nodding grimly at her. "Trust me; those things are _tough_; I've been taking ships out into the galaxy for fifteen years and I've only taken out about five of them-"

"Hold on; you've defeated _five _hive-ships?" Elizabeth interjected, her hope renewed at this latest discovery. "Could you maybe-"

"Give you some pointers?" John finished for her, looking regretfully over at her even before she finished the sentence. "Wish I could, but it's not as simple as 'fire here and the thing blows up'; you've got to find the _exact_ spot to hit if you want to cause the maximum possible amount of damage with the drone weapons- I was always out in the… gateships… when I fought them, so all I really had to rely on were the minimal drone weapons those things have to offer-, and those things are so large- not to mention the fact that I don't have any kind of 'plan' to point out where to aim at for your pilots before they get here- there's no way that any of your pilots could find that area in the kind of conditions we'd have to work with here."

"Conditions?" Elizabeth repeated curiously; even if it would be difficult to reveal the source of her information to Sumner, anything she could learn about Wraith tactics at this point couldn't fail to be useful. "What kind of… conditions are you talking about?"

"The Wraith never developed shield technology- given that their ships are fundamentally organic, it would have been difficult for them to incorporate that technology at best, and given that the Ancients' drone weapons are capable of penetrating any kind of defences it wouldn't really have accomplished anything in the long run-, but they came up with a pretty effective substitute," John explained, turning around to lean slightly against the balcony railing as he spoke to her. "In fights with other spaceships, their darts commonly fly around the hive ships in a kind of 'web' pattern to intercept any long-range weapons used against them; you try and use most conventional long-range missiles against them and you'll be more likely to strike a dart than to actually hit the hive ship itself. It took me a great deal of trial and error, combined with a _lot _of research- plus the fact that I had that whole cloaking thing to help me make sure nobody saw me-, to figure out what I needed to target if I was going to destroy those things, and I had the advantage of having practised a lot before I tried anything like that and possessing a fairly powerful Ancient gene… though I don't like to brag about it, of course."

"Of course," Elizabeth said, nodding in understanding even as she noted that one of the main theories about the Phantom had apparently been right; he _did _possess a powerful version of the Ancient gene (She knew that it might be a lie, but the casual manner in which he'd mentioned it suggested to Elizabeth that it was just something he'd grown so used to having that he barely thought about it any more). "So, in other words, we couldn't use your method ourselves because none of our pilots have the skill, control or training that you had when you were put in their position?"

"Yep," John confirmed, nodding with a slightly apologetic expression. "I mean, I might be able to _show _your men where to go, but I get the feeling Sumner wouldn't trust me in a gateship in a fight like _that_; with so many darts and gateships flying around up there, he wouldn't be able to keep an eye on me to make sure I'm doing what I 'should' be…"

For a moment, the Phantom simply stood silently on the balcony, staring out at the landscape before him as Elizabeth wondered what she should say at this point- his last comment certainly didn't make it easy for her; what did you say to a man who was so casual about the fact that he wouldn't be trusted?-, until he finally broke the silence. "Anyway, enough about that; I didn't just invite you out here because I wanted to talk."

"You didn't?" Elizabeth asked, looking at him curiously.

"Nope," John replied, as he reached into his cloak. "Actually, I wanted to give you something."

Before Elizabeth could ask why John wanted to give her another present so soon after the last one- her birthday had barely been a couple of weeks ago-, he had pulled out the object in question and tossed it to her, and she could easily see that it wasn't a conventional present, but what looked like a Life Signs Detector with an Ancient keypad.

"Uh… thanks," she said, looking at John in the hope that he'd explain the 'joke' behind the current gift.

"You're wondering why I gave you that, huh?" the man known as the Phantom said before the diplomat could ask the question herself, a slight smile on his face under his mask in a manner that Elizabeth was beginning to actually find kind of charming. "It's not the control pad that's the gift; it's what's _in _the pad that's what's important right now.

"What's… _in _it?" Elizabeth repeated, looking in confusion at the pad once more. "What do you mean?"

"It contains the computer program that features the only location of the password that will shut down the program I installed in the Atlantis computers that activate the shield whenever you attempt to dial any planet in the Milky Way galaxy," John replied, a casual smile on his face as if he was revealing nothing more groundbreaking than a weather report. "Just point it at the DHD- so long as you're within visual range of the DHD any other barriers are academic-, enter the same code you used to activate the grounding stations, and the program will be transmitted to the DHD and deactivate the feature that causes the shield to activate whenever you try to dial any planet in the Milky Way galaxy."

Elizabeth blinked in confusion.

"Hold on; a computer _program_?" she said, looking sceptically at him. "But we've already determined that the shield will be shut down with a _password_-"

"Which I programmed that device you're holding right now to select at random from the Ancient database when I originally added that particular feature to the shield's programming to prevent any Wraith from dialling Earth if they should gain control of Atlantis, subsequently leaving it in a safe place after programming it with an 'anti-Wraith-feature'," John explained, holding up a hand to cut Elizabeth off before she could ask any further questions. "A lot of effort to go to in order to get a password, I know, but it was the only way I could be sure I wouldn't give the Wraith the code if they somehow managed to find Atlantis and tried to torture it out of me; I couldn't _give _them what I didn't _know_."

"And that… 'anti-Wraith-feature' you mentioned this device possesses?" Elizabeth asked, looking uncertainly at the device in her hand.

"Oh, nothing to worry about; the thing's just designed to explode if anything with Wraith DNA tries to touch it to prevent _them _from using it to access Earth," John replied, smiling slightly at her before his face fell as a though occurred to him. "By the way, you'd better put it somewhere safe when you're done so that the Athosians don't get anywhere near it; I don't think it's _that _sensitive to Wraith DNA, but I'd rather not risk it-"

"Hold on; the _Athosians_?" Elizabeth asked, cutting John off as she glared critically at him. "What are you talking about; _they're _not Wraith…"

"Not _completely_, no, but a Wraith scientist performed experiments on some Athosians in the distant past in an attempt to improve the feeding process that resulted in Wraith DNA being introduced to their systems; that's how Teyla and some of her people are able to sense the Wraith when they're within range," John explained, his voice as casual as though he was revealing the latest weather report.

Noting Elizabeth's stunned expression at his latest revelation, however, John smiled reassuringly at her, raising one hand in a calming gesture. "It's not a _major _part of her genetic background, of course- Teyla isn't going to start wanting to feed on people or anything like that; she's limited to simply sensing the Wraith when they come too close due to her Wraith DNA allowing her to slightly sense their psychic network -, but I don't know precisely how sensitive the device is to Wraith DNA, and I'd rather not risk her setting it off and causing all kinds of awkward questions."

For a few moments, Elizabeth could only stare incredulously at the man who had just revealed something she couldn't believe.

Teyla and the Athosians had _Wraith _DNA…

"And… that doesn't bother you?" she said at last.

John blinked.

"Excuse me?" he asked, turning back to look curiously at her.

"Well… you fight the Wraith for… well, I'd say a living, but that implies you're getting paid for it… and you're not _remotely _concerned about the fact that you have someone with Wraith DNA in the city itself?" Elizabeth asked, looking at the man as she tried to gauge his reaction (The cloak and the mask really made it hard to read his body language, particularly in the current lighting). "It's just… well…"

"Given your prior experience with some military leaders you're wondering why I'm not instantly going all 'she's not human and must be banished from Atlantis', huh?" John replied, smiling in understanding at her as he shrugged. "Well, I don't deny that the thought of it freaked me out a _bit _when I first found out people like her existed, but after I checked over enough info in the Wraith lab where I learnt about them, I quickly determined that they're no real threat to anybody; the greatest risk is that a Wraith _might _be able to influence them over the telepathic network, and given how dormant the Wraith genes are that could only happen if one of them tried to deliberately 'hack' the network themselves."

"Right…" Elizabeth said, nodding thoughtfully at John's comments even as she inwardly thrilled at the implications of this latest discovery.

He didn't judge people by what they _were_… he judged them by what they _did_.

After so long dealing with Sumner's 'paranoia' when it came to anything Phantom-related simply because the Phantom was an unknown in this situation, or the mission reports she'd read while she was in charge of the SGC featuring references to people who were willing to do whatever it took to 'protect' Earth even if it meant hurting innocent people just because those people weren't 'human', it was…

Well, it was… nice… to meet someone who didn't care about a little thing like the other person not being entirely human.

"So… the Wraith don't know about this either?" she asked after a moment's pause, looking uncertainly at John as she tried to force such thoughts to the back of her mind; she had to stay _professional_.

"No, they don't; the scientist who carried out the experiment abandoned the project when he realised what had happened and every Wraith who knew about it assumed that the 'gift' would die out with interbreeding over the years," John replied, nodding briefly at her. "I found the lab where the experiments had taken place and managed to track the people he'd experimented on back to their home planets, but in general the results were always the same; there was no way for anyone to deliberately 'exploit' their access to the Wraith network unless they knew what they were doing, and even then they'd need to be in relatively close contact with a Wraith if they were going to have any chance at all of succeeding."

"I take it those exact circumstances weren't something that was particularly likely to happen?" Elizabeth asked, allowing herself a slight smile despite the seriousness of this latest discovery.

"Given the Wraith's habit of culling any inhabitable worlds that might be close enough to a hive-ship for the people in question to 'practise' their ability on… not really, no," John replied, shaking his head. "Besides, you have to take into account that most people wouldn't even realise what they were sensing; they'd just put it down to nightmares from the Wraith coming closer rather than them actually sensing the Wraiths' _thoughts_."

"True…" Elizabeth said, nodding briefly in acknowledgement of John's point before she looked back at him. "So… no point telling Teyla about this, I assume?"

"Not unless it becomes necessary for the city's continued survival to know what the Wraith are doing up there… _and_ not unless you can come up with a way to mention it without revealing _how _you know about it," John added, once again assuming his 'don't-tell' tone of voice that he always used when asking her not to mention that she'd spoken with him.

"Anyway," he said, indicating the door behind him, neatly cutting off any further attempts Elizabeth might have made at asking why her continued status as leader was so important to him, "you'd better get back in there and get that program transmitted into the DHD as soon as possible; the way things are going, the sooner you can get some back-up here the better."

"But-" Elizabeth began.

"I've already modified the program to simply shut the shield down when the next attempted password after it's activated is entered; as far as the technicians are concerned, they'll have discovered the password themselves," John said, evidently guessing what she was asking before she'd even finished asking the question. "Don't worry; nobody will know that you or I had anything to do with the shield being shut down."

After another brief silence, Elizabeth slipped the small pad into her pocket and smiled at him.

"Thanks," she said simply.

"No problem," John replied, as he indicated the door once again. "You'd better get going; the air in Atlantis isn't _that _bad."

Allowing herself a slight smile at that little 'joke'- it wasn't much of one, she knew, but in a situation like this anyone who could feel comfortable enough to say things like that was all right in her book-, Elizabeth walked back through the door, leaving John standing silently on the balcony as she headed for her office, pulling out the control pad even as she sat down.

_Here goes_… she thought to herself, as she aimed the device in the direction of the DHD and tapped the relevant buttons…

* * *

AN 2: Well, that's the shield issue sorted; next chapter begins the events of this universe's version of "Letters from Pegasus", including a little confrontation I've been looking forward to writing for some while now…


	28. I Don't Need To Listen to the List

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

The next morning's meeting with Colonel Sumner's team- accompanied by several senior members of the various departments currently operating in Atlantis- proved to be a far more cheerful encounter than any of the participants could have expected it to be. Only a few short hours ago, they had been sitting around trying to figure out a way of dealing with a situation that seemed to be virtually their own death certificate, and yet now, here they were, facing the genuine possibility that they might _just _be able to survive this upcoming nightmare after all.

Which, unfortunately, wasn't to say that it was a peaceful meeting; Elizabeth had long ago come to realise that, when it came to anything in the Pegasus Galaxy- particularly when it came to anything that remotely connected the Phantom and Colonel Sumner- all that she could do was prepare for the worst-case scenario, no matter how much she might hope for the best.

"So you're telling us that the shield just… shut down?" McKay asked, looking sceptically at Chuck- the technician who had been in charge of the control rook when the events that were the topic of the current meeting had taken place. "And you _think _that it wasn't your team that shut it off?"

"Uh… pretty much, yeah," Chuck replied, looking awkwardly around the room at the rest of the Atlantis senior staff. "I mean, I'd just been trying another password possibility from the database, so I _guess _it's possible that it could have been a delayed response…"

"Delayed by three _minutes_?" McKay said, looking sceptically at the technician. "I know you're not me, but everyone here knows that Ancient technology could _never _be that slow in this kind of condition; hell, even in the worst condition Ancient computers could _be _in without not actually being _able _to work, it should only take a minute- _two_, at most!- for them to respond!"

"So… you're saying that something _else_ was responsible for shutting down the shield?" Sumner asked, looking pointedly at the Canadian scientist before he turned to look at Chuck. "You're certain that you've dialled a Milky Way address?"

"We managed to make contact with no less than three planets in the Milky Way that have established diplomatic relations with the SGC; all of them were able to confirm that we had dialled our home galaxy, with no time dilation or any other such issue delaying our ability to send and receive radio signals through the wormhole," Chuck said, a brief expression of frustration at the implication in Sumner's statement as he glared at the colonel before he assumed a more casual expression as he turned to look at Elizabeth. "We concluded that it would be best to wait until we'd told you all about this latest turn of events before we tried to contact Earth directly; you know, in case anyone else in the expedition had anything they wanted to send along with the main message about what we're up against right now…"

"You did the right thing," Elizabeth said, nodding in understanding at the young man (She was _slightly _annoyed that the program to shut the shield down hadn't worked out the way John had said it would, but she supposed it was hardly his fault if he hadn't had the time to test that it would do what he'd told her it would accomplish; when would he have felt the need to test something like that when he'd probably assumed he'd have more time before the city found itself in this kind of situation?) before she turned to look at Colonel Sumner. "With this in mind, we should send a message to Earth detailing our current situation as soon as possible; even if they can't send us anything through the Stargate themselves, any information we can provide them with about our current situation might help them to provide us with something we can use against the Wraith."

"Agreed," Sumner said, nodding briefly at Elizabeth before he turned to look at McKay. "Doctor McKay, prepare all available information we possess on the Wraith for transmission to the SGC; the more information we can provide them with the better."

"As long as we're sending messages, we should let the rest of the city know what we're planning to attempt," Elizabeth added, looking pointedly at Sumner for a moment to make sure he didn't object to her decision- she was fairly certain that he'd allow the messages for morale purposes but she couldn't be certain- before continuing. "If any of them wish to send a message home, we should give them the opportunity to do so; I assume that adding in some personal messages would be possible, correct?" she asked, looking inquiringly over at McKay.

"Hey, I worked out a way to transmit a large portion of data in a micro-compression data burst a few years ago; if we had to I could send our mission reports and personal messages from everyone on-base in just over a _second_ and still have room left over to send a movie if I wanted," McKay said, smiling slightly smugly at her before he glanced back around the table. "Anyway, I'll do what I can about uploading the information from the Ancient databanks; in the meantime, maybe one of you could see about talking to the rest of the team? You know, let them know what's up, give them the opportunity to record a few messages, stuff like that…?"

"Good point," Sumner said, nodding briefly at the Canadian scientist before he turned to look at Ford. "Get on it, Lieutenant."

"Yes sir," Ford said, standing up and heading for the door to the conference room.

"Doctor McKay," Elizabeth continued, turning to look at the scientist, "have all your staff working on downloading all available information from the Ancient database as soon as possible; even if Earth can't send us any help, we have a duty to let them learn as much as what we've discovered here as we can."

"Check," McKay said, before he stood up to follow Ford out of the conference room, pausing briefly at the door to look back at the remaining three people in the room. "I'll let you know what I manage to download from the database when the time comes; if… well, if we can't come up with a decent plan to deal with the hive ships, I'd appreciate your input on what we decide to send back."

Elizabeth took a brief moment to collect herself- as much as she recognised the fact that they might have to abandon Atlantis to prevent the Wraith from gaining control of the city, she still hated to think about abandoning this incredible city unless they were certain they would have to do so-, before she nodded in understanding.

"Agreed," she said simply. "Call me when you reach that stage; I'll… I'll do what I can."

McKay briefly nodded in response, and then he turned around and walked out of the conference room leaving Elizabeth to turn and look at Sumner and Teyla.

"In the meantime," she said, turning the conversation back to an area where they could at least take some kind of action as she looked directly at Sumner, "we need to determine some way of getting a better look at these Wraith ships before they reach here; if we can gather a clearer picture of what we're up against we might be able to come up with a better idea of how to defeat them."

"I've already been thinking about that," Sumner said, nodding briefly at her in response. "I spoke with Doctor Zelenka and Sergeant Markham this morning before I came to the meeting; according to our sensors, the Wraith ships appear to be leaving and entering hyperspace at fairly regular intervals. Whether these pauses are the result of some flaw in their hyperdrives or simply them stopping to feed as they travel, Doctor Zelenka has been unable to determine, but he assures me that, regardless of the reasons for it, the regularity of their pauses means that he can identify a few locations where Teyla, Markham and I can travel via gateship to take a closer look at the hives while under cloak."

"A good strategy," Elizabeth said, nodding briefly at Sumner even as she wished he'd told her about that plan before he carried it out; his commitment to his military duties was commendable, but he sometimes seemed so dedicated to attending to the military side of things that he forgot that this was supposed to be a joint military/scientific expedition. "Just remember to be careful and stay out of sight; we can't afford to let the Wraith know that we're aware of their presence yet."

"I have already identified a suitable planet for us to observe the Wraith from," Teyla reassured her, taking up the explanation as she looked at Elizabeth after a confirming nod from Sumner. "My people have regularly traded with the people of one of the worlds that the Wraith shall pass by on their way here, and the Stargate's location is easily accessible by ship; Colonel Sumner and I feel that it is as suitable a location as any to observe the hive-ships from."

"Good to know," Elizabeth said, smiling slightly at the Athosian woman before she indicated the door to the conference room. "Get to it, but be sure to be back here as soon as possible; I want you here when we make contact with Stargate Command."

"Understood," Sumner said, before he stood up and looked over at Teyla. "Come on; let's go."

"Of course," Teyla said, standing up and nodding briefly at Elizabeth before she turned to follow Sumner out of the conference room, leaving Elizabeth alone to contemplate the most crucial issue the current situation left her with.

Specifically, if Atlantis faced destruction…

What would _John_ do about it?

Would he leave the city with them to continue his fight against the Wraith, trying to continue his apparent 'mission' to protect the Pegasus Galaxy even if it meant working with people who didn't trust him…

Or would he stay and fight off the Wraith until the city had exhausted the last of its drones- of which they didn't have that many to begin with; the Ancients must have virtually depleted their drone supply during the last days of the Ancient-Wraith War- and the few remaining dregs of power in the ZPM, at which point he'd probably destroy the city with himself still inside it to prevent the Wraith from gaining access to the Stargate.

She knew that the chances of John agreeing to the first were low at best- given Sumner's evident disdain of him so far, it was unlikely the expedition's military leader would even _consider _allowing the Phantom to leave with them if things reached that point-, but the thought of him choosing the second…

For some reason, just the _thought _of John dying was… painful.

In many ways, it hurt more than the thought that she'd never see Simon again…

_And where did _that _comparison come from_?

Shaking her head to force such thoughts aside- she had more vital matters to deal with right now than her fiancé back on Earth to a man who went around in a mask and a cloak-, Elizabeth walked out of the conference room herself, trying to force her mind back to the matter of sorting out what she would send in the message; condolences for the deaths of those who'd lost their lives so far was definitely near the top of the list, although sorting out the mission reports she'd received over the last few months would also have to take priority…

Plus, she'd need to go over her old reports to make sure she hadn't mentioned anything that might possibly reveal anything about her feel-_meetings_ with the Phantom; the last thing she wanted was General O'Neill questioning her judgement for personal reasons…

And _why _did she keep coming back to this?

* * *

As Doctor Kavanagh walked into his room later that night, he allowed himself a slight smile at the knowledge that he'd finally managed to voice his issues with the chain of command in Atlantis; even if they didn't get out of this situation- which, given the Wraith hive-ships currently bearing down on them, seemed to be the most likely final outcome of their current crisis-, at least everyone back on Earth would have an unbiased view of how things had been in Atlantis.

Quite frankly, he couldn't believe the lack of courage some people seemed to have when it came to confronting Doctor Weir about her actions; they'd been here for the better part of a year now, and yet as far as he could tell he was the _only _person to ever confront that woman about what she'd done _wrong _over that time period.

Why was it that none of the other members of this stupid expedition seemed to _care _about the fact that she'd put the city at risk for nothing more than a _slender_ chance of saving a handful of expedition members and a couple of primitive civilisations that would take at least decades before they could contribute anything more worthwhile than food to the expedition's current campaign against the Wraith? If they couldn't find anyone able to actually offer them some kind of help against the Wraith, as far as Kavanagh was concerned the city should just leave them to fend for themselves and keep on trying to form an alliance with somebody who could _offer _them something; trying to help every pathetic civilisation out there just depleted their resources and left them increasingly vulnerable.

If Doctor Weir had just made a _bit _more of an effort patch things up with the Genii after that last encounter with them- it wasn't like they couldn't get away with giving the Genii _some _C4 if it would improve their own situation-, then _maybe_-

"Doctor Kavanagh?" a voice said from off to the side of the room, breaking Kavanagh's train of thought.

"What the… how did you get in here?" Kavanagh asked, turning to look in frustration at the corner of the room where the voice had come from. "Does nobody have any respect for _privacy_ any more-?"

"When _you_ show no respect for the leader who has kept this expedition intact for the better part of the last year," the voice replied, as the speaker stepped out of the shadows to reveal a pitch-black cloak and a gleaming silver mask that did little to conceal the evident hostility in his stance, "why should anyone else show respect for a little thing like _that_?"

Kavanagh's eyes widened in horror as he realised just who was now standing in front of him.

_The Phantom_…

The man who had been running around through the city for the past few months, doing essentially whatever he wanted, regardless of the consequences to any of the expedition…

If there was one person in this city who frustrated Kavanagh more than Doctor Weir, it was this guy; he just waltzed in whenever the city was in trouble- often because of Doctor Weir's actions, such as when she chose to evacuate the city and rely on lightning strikes rather than the ZPM to protect them from the storm; they could have just as easily survived on the ZPM alone-, did what he wanted, and then walked away without even giving the expedition the slightest _hint _about what he wanted or where they could find something _useful _in this city…

And now, here he was, standing in Kavanagh's room, as casually as though he had done this before- that was a worrying thought; _had _this man sneaked into Kavanagh's room before for some reason?-, what looked like a gun just visible underneath his cloak- his right hand hovering over it in a manner that left Kavanagh feeling _very _uncomfortable-, and looking at him in a manner that made it fairly clear to the scientist that he was _not _going to like whatever reason the Phantom had for coming here.

"There are few things in this world I can tolerate less than the Wraith, Doctor Kavanagh," the Phantom said, his tone almost deceptively casual if one ignored the harsh glare in his eyes, "and one of them is when self-centred egomaniacs panic and complain about having to take a few risks simply because they feel that _they _are so important that people should consider _their _safety over everyone else's-"

"I was _not_-" Kavanagh began, taking a brief step forward before he paused mid-motion, the Phantom's weapon- which he had heard described in some reports of the Genii invasion as being capable of blowing peoples' _limbs _off- aimed directly at his face; the man had removed it from under his cloak so rapidly that Kavanagh had barely seen him move before it was right in front of him

"You mean you _haven't _been considering your safety over everyone else's?" the Phantom finished, an inquiring tone in his voice as he studied the man before him. "In that case, I would appreciate your explanation for your little 'speech' earlier while you were making your message for Earth, during which you listed what, in your opinion, were Doctor Weir's most significant 'mistakes' since she has arrived in Atlantis."

Kavanagh blinked in confusion.

"E-excuse me?" he asked, looking uncomfortably at the man before him (How could this guy know what he had said in his message; the room was soundproof and only he and Lieutenant Ford had been anywhere _near _that part of the city when he'd been recording his message for Stargate Command!).

"Well, I find it… interesting… how Doctor Weir's biggest 'mistakes', in your opinion- based on your little video message, anyway; it's possible there were other issues you have with her that you didn't mention because you recognise how self-centred they are-, are the ones that meant that you yourself would be at risk of getting hurt to even the _slightest _degree," the Phantom replied, shaking his head slightly as he stared at the scientist before him. "Whatever perspective I take to look at it, that seems very… self-centred… from where I'm standing."

"All I did was voice valid objections to her-" Kavanagh began, only briefly wondering how the Phantom could have known about that message; he'd only _recorded _the message about an _hour _ago.

"You objected to her decision to allow Sumner to try and rescue the captured Athosians; if things had gone wrong, the Wraith could have gained access to Atlantis," the Phantom interjected, not even allowing Kavanagh the common decency to finish his sentence before he continued to speak. "Her decision to allow the Stargate to remain open when the gateship was stuck half-way through it; weren't _you_ the one who thought that Atlantis should raise the shield and/or shut down the wormhole because there was a _chance_ that the ship had been so badly damaged that it would explode if Doctor McKay tried anything? Allowing the Athosians to join the expedition; there was a _chance _that they could be dangerous, even if subsequent events have proven to the contrary-"

"You have no _right_-" Kavanagh began, taking a step forward before the Phantom made a brief movement and suddenly Kavanagh found himself with a gun pointing at his face.

"I have lived in this city for over two decades, and am more aware of how this galaxy works in general- and how this city works in particular- than you could _ever _hope to be; I think you will find that this fact gives me _every _right to pass judgement on your petty complaints about how things have turned out for you in the last few _months_," the Phantom said, his eyes glaring at the doctor beneath the shadows caused by his mask. "I can assure you, Doctor Kavanagh I am _fully _aware of the circumstances responsible for why Eli-_Doctor Weir_- chose to take the actions she has taken up until this point, and _I_ can find no fault in her decisions. They have put Atlantis at risk, I do not deny that- after all, I have been here for twenty years without the Wraith even _looking _at this part of space and now they are sending at least _three _hive ships because of your expedition's actions-, but even with my experience I can think of nothing else that Doctor Weir could have done that would not have brought the Wraith down upon this city far faster while leaving this city with far less men to defend it."

After pausing for a moment, apparently solely to confirm that the man before him was listening to what he had to say, the Phantom continued to speak, his eyes glaring harshly at Kavanagh as his fingers flexed over the handle of his gun in a more-than-slightly-worrying manner. "You, on the other hand, would have been perfectly content to allow hundreds of innocent people to die so long as you yourself received what you wanted; I am certain that, were it up to you, this expedition would be stealing the ZPM from M7G-677 as we speak, solely to provide Atlantis with just a _fraction _more power, despite the fact that doing so would doom that planet's inhabitants to being culled."

"The technology we have here could save millions- _billions_ of lives!" Kavanagh countered, trying to strengthen his resolve as he stared back at the Phantom, refusing to allow himself to be intimidated by a man in a mask. "What do those… _kids _have to offer that we don't? We're the only people in this galaxy with any _idea _how this technology works-"

"You're right," the Phantom interjected.

Kavanagh blinked.

"You… you admit it?" he said, smiling slightly at the other man as he processed his last statement.

To actually hear someone _acknowledge _that he was right…

"To a point," the Phantom said, his eyes narrowing behind his mask as he looked at Kavanagh, dashing the scientist's brief hopes that he was dealing with someone who understood him. "Your peoples' knowledge of how Ancient technology works does put this expedition at a significant advantage over the rest of this galaxy, but as far as I am concerned, Kavanagh- and I am sure that there are many in this expedition who would agree with me, even if they do not trust my methods-, the lives of the children of M7G-677 are no less important than your life."

"But we-" Kavanagh began.

"You cannot _fight _creatures such as the Wraith by sacrificing that which _separates _you from them," the Phantom said, his voice cold and his tone low as he kept his eyes fixed on the scientist. "I do not care how smart you think you are, how strong you are, how many weapons you possess… as far as I'm concerned, one life is just as important as any other."

Despite himself, Kavanagh snorted at the hypocrisy of the man before him.

"You expect me to believe _that _after you killed all those Genii a few months ago?" he asked, his nerve apparently restored at the opportunity to point out the flaws in the Phantom's argument; after so long dealing with the 'legend' this man had left behind him, he would be damned if he wasn't going to take advantage of the current opportunity available to him to give the arrogant son of a bitch a piece of his mind. "You killed over _sixty _people-"

"There is a difference between killing those who would be willing to kill _you _and being responsible for the deaths of those who seek nothing more than friendship and protection from the nightmare that you _all_ face, simply because you feel that you are more 'important' than they are," the Phantom said, his eyes narrowing even further as he glared resolutely at the man before him. "I have heard a saying in my time here that I have taken to heart; take care when you fight monsters, lest you become a monster yourself."

"Which has… _what _to do with anything?" Kavanagh asked, glaring back at the man before him.

"A monster is someone who takes life with no thought whatsoever for those whom they kill; for me, the worst kind of monster is the one that would cause harm, whether directly or indirectly, to others, for no other purpose than to accomplish their own goals," the Phantom said simply. "Doctor Weir's choices have been dangerous, I will grant you that, but all of them have been necessary for the city to survive long enough to reach this point… and she has _never _compromised on morality, whereas _you _appear to be perfectly willing to do so if you only had the authority."

For a moment, as the Phantom paused while glaring at him resolutely, his fingers flexing around his gun, Kavanagh briefly wondered if the man was going to shoot him…

Then there was a sudden brief, blinding pain in Kavanagh's cheek, and he glanced up just in time to see the Phantom slipping an arm back under his cloak and realise that he'd just been punched.

"Exploration through the Stargate is an incredible experience, Doctor Kavanagh, but it is _not_ a safe one; if you wished to remain safe, you should have stayed back on Earth," the Phantom said, his tone cold as he glared at the scientist. "Perfection in this situation is impossible; Doctor Weir has done what she could do in a new situation with no prior experience, and you are _far _from being in a position to criticise her when you have no understanding of what must be confronted to survive in this situation."

Walking over to stand above Kavanagh, he crouched down and grabbed the scientist by the collar, subsequently lifting him up so that the two men were nose-to-nose.

"Therefore," the Phantom said, his eyes narrowing behind his mask as he glared at Kavanagh, "seeing as how you are an arrogant, spineless little _toad_ who cannot even have the nerve to voice his complaints about his leaders to their _faces_, but still retain enough humanity or lack the nerve to avoid actually _doing _any of the things you 'think' this city should do to survive, I will give you this opportunity; take the opportunity to actually send a message to anyone back home that you actually _care _about- assuming there's anyone who fits _that _category for you, of course-, and then either show some _backbone _or get out of Atlantis, because I will _not _have cowards in my city. Understood?"

Kavanagh could only nod, even as he fumed at the man's arrogance; he was _one man_, and he thought that _he _had a greater right to this city than _they _did?

"Good," the Phantom said, standing up with a slight smile on his face, his arm shifting his cloak slightly to reveal his gun at his side once again; evidently he wanted to make sure that Kavanagh wasn't tempted to try anything as he left. "Think on what I have said once you wake up; have a pleasant evening."

Kavanagh barely had time to process what had just been said before he heard what sounded like something charging up, followed rapidly by a sound that he was prepared to bet was an energy weapon firing before blackness took over his brain.

* * *

As Kavanagh fell to the ground, reendered unconscious by the stun-blast, John allowed himself a slight smile.

_That went well_, he mused to himself, quickly slipping his gun back into its holster before he turned around and crouched down to open the small door that would lead him back into Atlantis's maintenance tunnels; it wasn't the most comfortable of locations, but he'd really grown used to these things after a while.

He knew that it was a bit of a risk to show up just to tell Kavanagh to either shape up or ship out, but he couldn't help it; that guy's constant 'complaints' about Elizabeth _really _got on his nerves, and he'd just reached the point where he'd wanted to give the guy a piece of his mind.

Besides, he doubted that he really had anything to worry about; Kavanagh was such a pathetic coward that he'd never _dare _to tell anyone about this particular meeting in case it increased his chances of getting a 'return visit' from the Phantom which might result in him receiving something more… permanent… from the gun than a stun-blast…

_Too bad that's the last fun I'll have in a while_…

* * *

AN: Well, now that I've given that arrogant twat a piece of my mind- what can I say; Kavanagh's just one of those characters who REALLY got on my nerves-, next chapter features them contacting the SGC and learning about the situation at that end of the galaxy


	29. Calls to the Milky Way

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

The next morning, as Elizabeth stood on the balcony of the control room, McKay tapping away at the computers he'd set up in preparation for sending the data and messages through to the other side after they'd made contact with Stargate Command, she wished that she could feel better about this situation than she actually did.

Even if they were able to send a message through to Earth, they still had no real guarantee that it would make any difference to their current plight. With Atlantis's only remaining ZPM as low on power as it was, their chances of fighting off three Wraith hive-ships were minimal at best, given their low amount of drone weapons- McKay had only recently managed to take inventory of the city's weapons supplies after they'd discovered the hive-ships approaching them; they assumed that the Ancients had used up the original supply during the last Wraith siege- and the sheer distance between Earth and Atlantis, the expedition seemed to be pressed for options even in a best-case-scenario…

But, on the other hand, they would at least have _tried _to do something to save Atlantis; even if Earth couldn't do anything, the expedition would have access to greater resources to deal with the problem than they had at present.

In the end, the one thing she mainly regretted right now was that so few of the people she'd sent condolence messages to knew the full details of what their relatives had been up to; it just seemed… _wrong _to her that so many people would never know the full details of what their loved ones had helped humanity accomplish before their deaths…

Right now, however, she couldn't allow herself to think about that; there wasn't time to think about what should be or might have been, no matter how much she might regret the losses the expedition had suffered to reach this point.

The best thing she could do was to focus on the fact that they finally had an opportunity to pass on what they had learned in Atlantis to Earth; regrets like that would have to wait until she could be certain that their sacrifice hadn't been in vain.

Looking resolutely around at the rest of her senior staff, Elizabeth nodded at Chuck as he sat in front of the controls.

"Dial the gate," she said simply.

Nodding in response, Chuck turned around and quickly entered the address for Earth into the DHD, everyone within the control room watching and waiting as the various chevrons illuminated on the Stargate before them, each of them secretly crossing their fingers as the seventh chevron was dialled…

Then, as the eighth chevron finally slid into place and the wormhole activated, with no sign of the shield being raised to prevent any attempts to send messages through to the other side.

As the various expedition members cheered and exchanged everything from high-fives to hugs with each other- even Sumner seemed to grin as he gave McKay an almost-affectionate thump on the back-, Elizabeth waited for the cheering to die down before she nodded over at Chuck to activate the radio that would transmit the message through to the other side of the inter-galactic wormhole they'd just created.

"Stargate Command," she said, trying to stop herself from smiling like a giddy schoolgirl (She had nothing against her team showing their enthusiasm at this latest turn of events, but she had to at least _try _and act professional if she had any hope of maintaining Sumner's respect), "this is Atlantis; I hope everything's well over there?"

For a moment there was silence at the other end of the radio link they'd just established, until the familiar sound of the SGC's commander finally responded.

"_Sorry, I was doing some paperwork; this is _Atlantis_ talking here, right_?" General Jack O'Neill's familiar voice said from the other end of the wormhole, evidently slightly sceptical about what he must have just learned about. "_Cause I gotta tell you, _really _not in the mood for a prank right now; I swear those things _breed _if left alone_…"

"No worries about it being a prank or mistake, General; you heard correctly," Elizabeth said, allowing the smile to spread across her face at the realisation that she was genuinely talking to Stargate Command once again. "This is Atlantis, with greetings from the Pegasus Galaxy; it's good to hear your voice again, General O'Neill."

"_Really_?" General O'Neill replied, sounding like he was currently in possession of a more-than-slight grin himself at the confirmation that they were there. "_Good thing you called when you did, if that's what you wanted to hear; I'm transferring up to Washington in a couple of weeks_."

"Washington?" Elizabeth repeated, unable to stop her slight surprise at that last comment; from what she'd seen of Jack O'Neill in action she would have sworn that nothing short of death could drag him away from Stargate Command.

"_Yeah, crazy, I know, but with the Goa'uld essentially useless now that the Jaffa have all quit and Anubis is dead there's really not much call for me down here, and with General Hammond retiring at the end of the month, the brass decided that I'd do better up there running Homeworld Security than sticking around here_," General O'Neill responded, sounding for all the world as though he was just discussing the weather rather than the news that the Goa'uld-

"I'm sorry, did you say that the Goa'uld are 'essentially useless'?" she repeated, looking slightly uncertainly at the radio in absence of being able to look at General O'Neill himself, her thoughts finally catching up to her mouth. "As in… they've been _defeated_?"

"_As good as, anyway; last we saw of them Anubis was stuck in eternal struggle somewhere on the higher planes of existence while Ba'al ran like a rabbit after his own Jaffa turned on him_," General O'Neill replied, the nonchalant tone in his voice one that Elizabeth had grown to know fairly well during their all-too-brief time working together at the SGC (She might have spent a few months in the role, but given that then-Colonel O'Neill had spent most of her time in charge frozen in an Ancient stasis pod, followed by her moving down to Antarctica to oversee work at the Ancient outpost, opportunities to talk with him had naturally been limited). "_All in all, it's really fairly quiet back here… but something tells me that the same can't be said for your group over there, huh_?"

"You'd be correct in that assumption, General O'Neill," Colonel Sumner said, stepping forward to better address the radio; evidently he had concluded that it was his turn to take control given the military nature of the current crisis. "We have a fairly serious situation here. Atlantis has only a limited amount of its full potential offensive and defensive capabilities, as well as possessing only a fairly limited power supply, and we have three enemy vessels that are each the size of islands on their own due to arrive at our location in the next couple of weeks."

After a moment's silence at the other end of the radio, General O'Neill finally spoke again.

"_You _really _don't do things halfway when you get in trouble over there, do you_?" he said, somehow managing to sound amused and frustrated at this latest turn of events simultaneously. "_So, what kind of bad guys are we talking about here_?"

"You'll find your answers to that in the download we're sending to you," Elizabeth said, taking up the conversation once again after a brief glance at Sumner. "We're sending you everything we've gathered about our current enemy, along with records of everything that we've been able to download from the Ancient database that might be of interest to anyone else; if the situation here proves unsalvageable, we wanted to try and preserve as much of what we've learned here as we could."

"_Let's hope it's not needed_…" General O'Neill said, sounding like he was only partly addressing the radio with that last comment before his voice resumed its original volume, most likely as he turned back to directly address the radio at his end. "_All right, send through what you've got; I'll have Carter and Daniel look over it all as soon as possible and we'll get back to you when we can_."

"Don't take too long; we've got… well, we're operating under a time limit, to say the least," Elizabeth said. "We'll contact you again tomorrow at around this time; everything we know about our current enemy is available in the files, along with other information such as our current situation in terms of power and defensive capability; we also included some personal messages some of the expedition members have prepared for their families at the end of the download."

"_Gotcha_," General O'Neill said, pausing briefly to apparently speak to someone else at his end- Elizabeth couldn't make out the precise words, but she could definitely hear the general's voice as he spoke to someone else- before his attention turned back to them. "_Send it through; we're all ready over here_."

Nodding over at McKay, Elizabeth waited for a few seconds to allow McKay to transmit the data in question before turning back to face the radio, waiting for a few seconds before General O'Neill spoke again.

"_OK, we've got that at this end_," he said, sounding once again like he was smiling slightly as he spoke. "_I'll have Daniel and Carter check over everything they can- and get the messages sent off to the relevant people- and get back to you tomorrow; no point wasting energy for a long-distance call if you've got the bad guys heading towards you already, huh_?"

"No, probably not," Elizabeth admitted, shaking her head slightly as she allowed herself a small smile at General O'Neill's simplistic assessment of their current method of communication. "We'll talk to you tomorrow, General."

"_Looking forward to it_," General O'Neill replied, shortly before Chuck terminated the connection, leaving the expedition members exchanging broad grins with each other at this latest turn of events.

They might still have some way to go before they could officially consider Atlantis saved, but they weren't alone any more; after learning of the odds that hey faced since coming here, anything that increased their chances of victory in the upcoming fight was welcome, no matter how slight a chance it was.

They'd done what they could; from here on in, the ball was in the SGC's court.

* * *

The next day, a new group of technicians gathered in the operating room along with the senior staff, the Stargate was dialled for Earth once again, the wormhole once again being established with no sign of the shield activating to block signals. It didn't attract as much attention this time around as it had yesterday- with so many incredible things to find in Atlantis, coupled with how little time they had until the Wraith arrived, everyone was busy doing what they could to explore the city before they were forced to leave it-, but those who were there were nevertheless grateful to see the wormhole connect once again as the link to Earth was established once more.

"Stargate Command," Elizabeth said, addressing the radio once again, "this is Atlantis; how's everything at your end?"

"_Well, still having a bit of trouble sorting out mission plans without an actual bad guy to fight these days- I was never wild about the survey missions when I only had to worry about arranging _one _of them at a time, never mind all the ones we've got going on right now-, but hey; whoever complained about _not _being at war_?" General O'Neill replied, his tone becoming more solemn as he continued. "_I'm just sorry we can't trade off some of our good luck at this end to you guys; sounds like you've got a _serious _problem waiting for you over there with those 'Wraith' things_…"

"A 'serious problem' is an understatement, General O'Neill," Colonel Sumner said, stepping forward slightly to subtly-yet-significantly push Elizabeth aside to speak to the microphone himself. "We have three hive-ships at least the size of Atlantis heading towards us, a seriously limited supply of drones, limited aerial combat vehicles, and our only power source barely has enough energy to defend us for more than a few hours… and that's even _without _taking the Phantom into account-"

"_Yeah, regarding that 'Phantom' guy; any chance you could see about asking him to help out over there_?" General O'Neill cut in, breaking Sumner off before he could go any further (A fact that Elizbaeth was grateful for; she really wasn't in the mood to hear _another _of Sumner's anti-Phantom rants after things had been going so well for her lately).

As Elizabeth took in the suddenly incredulous expression on Sumner's face, she had to cover her mouth to stop herself from laughing; the stunned expression on Sumner's face made him look like he'd just walked into a room only to discover he was dressed as a clown (Or something equally ridiculous along those lines).

"A… ask the _Phantom _to _help_?" Sumner repeated, staring at the microphone as though waiting for the punchline to a joke he hadn't understood at first. "General, with all due respect, the Phantom is-"

"'_A rogue element in an already volatile situation that must be contained before his vigilante-style actions jeopardise the city in a crisis situation', correct_?" General O'Neill said, clearly reading a transcript of a report that Sumner must have sent in the transmission. "_All valid points, Colonel- in a situation like the one you're in, you _do _need to be sure you know what everyone's doing-, but you're overlooking one crucial detail_."

"Which is?" Sumner asked, looking at the radio with an expression that made Elizabeth think that he would have called General O'Neill insane if he wasn't Sumner's official superior.

"_This guy seems to know more about Ancient tech than anyone else we've got- with you guys _or _at our end-, as well as apparently being able to do stuff with the control chair and other various doohickeys that we can only _dream _about pulling off, based on what I've read about him so far; can you honestly say we _couldn't _use that_?" General O'Neill asked. "_I get your concerns about him, but so far the guy really hasn't _done _anything that wasn't fundamentally to your benefit; if he hasn't tried to hurt you so far- as well as taking into account how fast he was at taking out that nanovirus thing you dealt with a few months ago-, seems to me like he's the kind of guy who might be interested in helping you out when things get ugly_."

For a moment Sumner simply stood in silence, staring at the radio before him, his expression reflecting a lifetime's faith in the chain of command simultaneously dictating that he comply with his superior's 'orders'- even if it was more of a recommendation than an actual order- and object to having to work with someone of unknown agenda and motives. Elizabeth had just started to wonder if she should say something herself before Sumner stepped up to the radio once again and simply said "Understood," before stepping back, clearly considering the matter closed.

"_Good_," General O'Neill said, clearly grateful to have that issue sorted out, before he turned his attention back to Elizabeth. "_Anyway, with that out of the way, you might like to know that Carter and Daniel have been over everything you sent us from the Ancient database with the intellectual equivalent of those brush things Daniel always uses when he's studying runes, and we've definitely got a _lot _of stuff to be going on with even if you don't manage to protect the city itself_," General O'Neill said, even as his tone made it clear that they weren't going to give up Atlantis as easily as his words might suggest. "_Actually, we might be able to help you as far as holding the city goes; we recently discovered an almost-fully-charged ZPM from a dig in Egypt that might be useful to you guys as a power source-_."

"Hold on; Egypt?" McKay repeated, stepping forward to stare in shock at the radio, breaking the silence that he'd maintained since the connection had been established. "There was a ZedPM in _Egypt_?"

"_Yeah, I know; amazing how much stuff people left us with when you start looking for 'em_," General O'Neill confirmed, his tone once again reflecting his usual casual sense of humour despite . "_Anyway, we were planning on keeping it around at this end in case we needed it- you know, a power source for the Antarctic outpost, something like that-, but given what you're up against over there, and given that we don't _really _have anyone to worry about back here, everyone here's already fairly certain you guys'll be getting it instead_."

"Uh… no offence, General, but as much as we appreciate the offer, that _really _doesn't help us much," McKay said, evidently making an effort not to sound ungrateful (Elizabeth briefly thought about objecting to his actions, but decided against it; if ZPM-related issues were the topic of the current conversation, McKay was unquestionably the best man to talk things over right now). "I mean, you can't exactly send it through to us from _your _end because you need the ZedPM's power to _dial _our address, and …"

"_No worries on that front; _Prometheus _might be a bit busy at the moment, but we've got the _Daedalus _pretty much sorted and ready to go any minute now_," General O'Neill replied.

"Daedalus?" McKay repeated, his eyes widening in surprise.

"_Daedalus_?" Sumner asked, looking inquiringly over at the city's chief scientist.

"Sister-ship to the _Prometheus_; I looked over some of the plans back when I was still on Earth," McKay said briefly, before turning his attention back to the radio. "I didn't even know it was finished yet; even allowing for the progress that must have happened since we left I thought it would be at least another few months before it was completed…"

"_We've managed to call in a few favours from our offworld allies to help out with construction over the last year since you left; all we need now is to get the hyperdrive finished and everything's good_," General O'Neill explained. "_Actually, from what I've heard part of the reason we need a bit more time is that we need to hook a few extras up to let _Daedalus _use the ZPM as a power source, and Carter says she could be there in a few days at maximum hyperdrive with _that _amount of extra 'oomph'_."

"Just how long will that take?" Elizabeth asked, looking uncertainly at the radio.

"_Well… _that _bit will take the better part of a week- maybe a little longer; turns out ZPMs're fairly tricky things to link up to-, but from what you've said in your reports you can wait for that long, right_?" General O'Neill added, evidently apologetic that he wasn't able to get anyone there faster than that. "_I'll see about getting a team together at this end to provide you guys with some extra manpower before we dispatch _Daedalus_, but with this kind of timeframe to coordinate a rescue effort I can't promise much more than a few dozen marines and some railguns, and even _that _might be pushing it_…"

"Anyone you can send would be welcome, General O'Neill; we appreciate your assistance," Sumner said, taking up the conversation once again. "We've got a couple of defensive measures we can take at this end already, but further manpower would certainly increase our chances."

"_Gotcha; just do what you can over there and we'll get back to you when we're ready to send back-up_," General O'Neill replied. "_Wish I could say I'll be there when we reach that point, but it'll pretty much be time for me to be briefing the new guy at that point anyway; I won't really have much time to chat at that stage_."

"Just so long as you send us some people when we need them we'll be satisfied, General," Elizabeth said, smiling slightly at the radio. "We've got a few possibilities we're trying to explore at this end to increase our chances, but any aid you can offer would be appreciated; we'll call you if we need you."

"_Gotcha_," General O'Neill replied. "_Don't call us- unless it's _really _bad-, we'll call you_."

With that, the wormhole connection was terminated, leaving the group standing silently in the control room for a moment, their hope restored by the news of the SGC's knowledge and plans to aid them in the current crisis, until Elizabeth turned to face them.

"All right," she said, her voice clear as she spoke, "we have reinforcements on their way, but that doesn't mean we can afford to slacken the pace as far as figuring out means of defending ourselves at this end goes. Study everything we have on the hive-ships' strengths and weaknesses and then see if we can find out anything further about Atlantis's defences; if there's even the slightest _rumour _of a weapons system we can use to increase our chances of success right now, I want it up and running as soon as possible."

"Understood, Doctor Weir," Sumner said, nodding briefly at her before he turned back to look at the scientists. "OK, people; let's _move_!"

Even as the scientists and soldiers turned around to leave the control room and return to their unofficially-appointed task of 'search Atlantis for anything potentially useful', Elizabeth couldn't stop her mind from focusing on one thought.

_General O'Neill was willing to accept aid from the Phantom_.

Did that mean she'd be receiving another visit from John soon…?

And why was that so _important _to her?

* * *

From his usual observation post in the control room, the man known only to Elizabeth Weir by the name of 'John' silently sat and watched her as she and her team began to make plans and preparations for the upcoming battle with the Wraith.

He had to admit, things weren't going too badly at this point. They'd made contact with Earth, the SGC were aware of the situation here and were taking steps to send help, they still had a decent length of time before the Wraith ships got here, and- the most encouraging news, in his opinion-, General Jack O'Neill- a man the elder Elizabeth had spoken of with a not-insignificant amount of admiration, from what he recalled; the guy had done some pretty impressive stuff as the leader of SG-1 before she came to Atlantis- had essentially told Sumner that the guy was to allow him to work _with _the expedition, rather than telling Sumner to capture him.

If nothing else, at least John knew _some _people in the military understood that he wasn't intending to harm anybody on the expedition.

He just wished that he could have faith that Sumner wouldn't put a 'creative twist' on General O'Neill's orders and try and confine him to that cell where they'd kept their Wraith prisoner- seriously, Sumner could have _really _showed more imagination in naming that guy; personally he'd thought about calling the guy 'Steve' or something like that- and justify it as requiring 'unrestricted access to his knowledge' or something like that.

John couldn't do that.

His knowledge about Atlantis would be beneficial to the expedition, he wasn't denying that, but he had to be free if he was going to make any kind of active contribution. Sticking in the cell and keeping him under control might be preferable to Sumner- at least that way he could be certain that John wasn't doing anything that he didn't know about-, but John had no illusions that Sumner would let him out afterwards; once he was in that cell, he'd be staying there.

He couldn't allow Sumner to do that to him; once the Wraith got here, he'd need to provide hands-on information about the enemy's tactics and technical capabilities, to say nothing of him being able to use the control chair better than anyone else in the city.

It might be fundamentally selfish, but he had no choice; if he tried to contact Sumner now, he'd just end up stuck in a cell at best and _ignored_ and put in a cell at worst.

For the moment, he'd just keep in touch with Elizabeth until the time was right, offer what advice he had available to him, and hope that was enough.

As he looked at Elizabeth as she stood in front of the control console, looking solemnly around at her staff as they hurried to fulfil their allocated tasks, he gave her a slight smile.

_You'll be fine, Elizabeth_, he promised her. _Just keep it together until I can do what I can_.

With that last thought, he turned around and crawled back into the tunnel, already planning out his strategy until the hive-ships reached the point where immediate action _had _to be taken…


	30. It's Crazy, But I Believe

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: OK, with us moving into the "Siege" storyline, I would just like to make one detail clear; 'Bob the Wraith' is NOT on Atlantis at this point, thus leaving Teyla completely unaware of her Wraith DNA and therefore ignorant of her ability to tap into the Wraiths' psychic network

The Phantom of Atlantis

Over the course of the next week, as the hive-ships advanced ever closer towards Atlantis, Elizabeth found herself facing all kinds of decisions as her staff made further discoveries about the city's potential defences. Sumner made sure that every available qualified pilot received the necessary practise to effectively pilot the puddle jumpers in the event of a combat situation- in an aerial assault mobile weaponry couldn't fail to be useful, and it had already been determined that it only took one drone to take out the Wraith darts-, Teyla and the Athosians did what they could to prepare for close-quarter combat in the event the Wraith managed to gain access to the city, and McKay and his science team went over everything they could find in the Ancient database seeking further information about possible defences the city had beyond the drones and the shield.

Ironically, it was at moments like this that Elizabeth realised how fundamentally little she had to do on a day without 'gate travel. While she was still in charge of looking over reports from the various staff members regarding what they'd discovered and whether it could be used against the Wraith when they arrived in Atlantis, in the end that was the extent of her involvement in the city's defences at this time. With no way of knowing if the Wraith would send further Darts to try and 'soften them up' like they had sent that first Dart earlier, Sumner had cancelled all offworld travels for the moment- particularly since their efforts to locate a potential Alpha Site were now unnecessary due to the ability to return to Earth having been restored to them-, distributing his men across various areas of the city to better coordinate an effective defensive stance against the Wraith, leaving Elizabeth with no real role other than to approve Sumner's transference of various personnel to certain areas, as well as other such matters as arranging for the city civilians to receive the maximum amount of training in the use of the available weapons in case the Wraith actually managed to get troops inside Atlantis.

All in all, apart from granting approval for various scientific and military matters that she only had a basic understanding of to begin with, the only other activity Elizabeth presently had to occupy her time was something she would never have admitted to anyone else; waiting for John to try and make contact.

She knew that it was essentially pathetic- here she was, a grown woman, and she was waiting for a guy to call her like some schoolgirl who'd just had a date with the star quarterback-, but it wasn't _just _personal reasons that kept her waiting (Even if a part of her mind kept on taunting her with the knowledge that they _did _play a big part in what she'd done); if the Wraith _did_ attack, John was far and away the most experienced user of Ancient technology they had available to them. If he could just be persuaded to help them in a more public manner than he'd been helping them up to this point- maybe even helping Sumner coordinate the defences; Elizabeth had little doubt that John wouldn't be that interested in taking orders after so long alone, but he might be willing to consider a partnership of sorts-, his aid could make all the difference…

However, by the sixth day since they'd made contact with the SGC, John still hadn't come to talk to her- whether because he had nothing to say or because he was waiting for the right moment, Elizabeth didn't know-, with the hive-ships now only about two days away from Atlantis, that McKay finally revealed what he and his team had been looking into since she and Sumner had initially given the scientists their various tasks.

* * *

"The defence satellite?" Elizabeth repeated, looking sceptically at McKay after the Canadian scientist had explained his latest proposed solution to her. "It took you _this _long to think of that?"

"Well, it would have been quicker, but Doctor Gaul insisted on checking everything over before we came to you; he wanted to be sure we didn't forget anything we'd picked up in our surveys that might have altered our plans," McKay said, waving a hand dismissively before he continued his speech. "Anyway, the point is, based on what research we've been able to do- what with the obvious distraction of having to investigate that crashed Wraith ship and Sumner preferring to figure out what we've got access to _here_ rather than _there_-, we're pretty certain that the only thing actually _wrong _with it is a lack of power; a single naquadah generator should be enough to get everything working in time to start firing at the Wraith when they pass by the satellite."

"And you're sure they'll go along this route?" Elizabeth asked, looking pointedly at McKay. "I admit astrophysics isn't my strong point, but there's a lot of special routes out there for the Wraith to approach Atlantis by; why would they deliberately go past an Ancient weapons platform, even a supposedly obsolete one, when there are so many other ways they could reach us?"

"Well, in a nutshell, the satellite's located at one of many points around this solar system where gravitational forces come together to create relatively stationary points for the Wraith to travel along; I'd go into more detail, but that would require giving you more background information about astrophysics than we can realistically be expected to cover right now," McKay said, waving a hand slightly dismissively before he continued. "The point is, the Wraith _will _pass by this satellite, and we're confident that we've learned enough about how it works to bring it back."

"And, in your opinion, all that's wrong with it is that it's out of power?" Elizabeth asked.

"Precisely," Doctor Gaul confirmed, nodding at her as he took up the explanation. "While the generators aren't enough to operate Atlantis's weapons systems without what power we have left in our current ZPM, the satellite requires far less power to operate successfully given its relative simplicity; after all, the Ancients' only real disadvantage in the last Wraith war was sheer weight of numbers rather than any kind of technological advantage…"

Elizabeth raised a hand to cut Doctor Gaul off before he started going into any further detail; while she appreciated enthusiasm, right now they really didn't have the time to indulge him.

"All right," she said, looking between the two scientists. "What do you need?"

"The satellite's fifteen hours away by gateship," McKay replied. "I recommend a small crew; the two of us plus a pilot."

"I'm fairly sure I can convince Colonel Sumner to lend you Miller for this; will that do?" Elizabeth asked.

"That should be fine," McKay confirmed. "Just so long as we get going soon; the hive ships will be in range of the satellite in forty-nine hours, and we're gonna need every last _second_ of that time to get it back up and running."

"Understood," Elizabeth said, nodding at the two men before her. "Get to work."

With that, the two scientists stood up and walked out of the room, leaving Elizabeth looking after them with a slight smile.

It wasn't much of a shift in their favour, of course, but right now she'd take any advantage she could get.

And speaking of advantages…

She paused slightly as a thought occurred to her.

She'd spent so much time waiting for John to contact her…

But what if she set up a situation to make it _easier _for him to do so? After all, she hadn't been out of her office for the last couple of days except to go back to her quarters to sleep… maybe if she headed out to her balcony…

It might appear arrogant to assume that he was watching her at the moment, but Elizabeth simply considered it practical; given John's evident desire to protect Atlantis, it only made sense that he was currently hiding somewhere where he could monitor any plans that the expedition might be coming up with to protect the city, which meant that he was almost certainly currently somewhere where he could keep an eye on her office and the conference room to allow him to listen in on the plans and subsequently contact her in case he had any further information to add to them.

He might not have anything he felt he _needed _to say to her right now, but that didn't mean she wouldn't appreciate a quick word with him to make sure there wasn't something else they could be doing.

(OK, so she also wanted to see him just for the sake of seeing him; after the effort she'd put into her work so far she felt as though she deserved to have some time off).

Her mind made up, sighing slightly in frustration to add to the impression she now sought to create for anyone else watching her, Elizabeth stood up from her desk and walked out of her office, heading for the balcony after a quick, brief conversation with Chuck to make sure he knew where she'd be in case something urgent came up (As well as giving him instructions to knock if her presence was required, her excuse being that she preferred to be alone right now without any thoughts of potential distractions).

As soon as she'd stepped out onto the balcony that was rapidly becoming her 'private' area in the city, she walked over to the edge, staring silently out at the moonlit ocean before her, before she spoke once again.

"Do you do the sneaking thing because you're used to it, or because you just like to try and surprise me?" she asked, a slight smile on her lips as she heard a low curse being muttered by somebody behind her.

"How did you know?" the now-familiar voice of John Sheppard asked, clearly stunned that she'd detected his presence.

"I didn't," Elizabeth replied, unable to stop herself smiling slightly as she turned around to look at him. "You're just starting to become predictable; if I'm out here and there's some reason you need to talk to me, you'll be here soon enough."

For a moment, John simply stared silently at her, before he chuckled slightly and walked out of the corner to stand alongside her.

"You're good," he said simply.

"I had to know how people would act in my line of work," Elizabeth said simply, before she shook off the smile and looked at John with a more serious expression. "Anyway, I take it you can guess that I want to talk to you?"

"A committed workaholic like yourself coming outside for some fresh air with Wraith hive-ships only around two days away from Atlantis?" John replied, a slight smile on his face under his mask. "The odds weren't exactly in favour of you coming outside for the goodness of your own health; you _had _to have another objective, really."

"And the reason you never bothered to contact me earlier…?" Elizabeth asked, looking back at him with an expression that combined an inquiry with a slightly teasing smile to reassure him that she didn't mind about the lack of contact.

"Well," John said, looking slightly awkwardly at her, "given that the Wraith are on their way, I've already decided to make contact with Sumner when they get close enough to be an issue; it's just that…"

"At the moment you can't be certain he won't just throw you in the cells the second you're standing in front of him, so you're waiting until he _has _to accept your help to talk to him?" Elizabeth finished, nodding in understanding at John. His motives might seem selfish- he was trading away potential opportunities to give Colonel Sumner advice about how to secure the city in favour of maintaining his own freedom-, but Elizabeth knew enough about him and Sumner to recognise that he was only doing what he felt he had to do. Given Sumner's repeatedly-stated dislike of John's independence, he'd most likely throw John in a cell as soon as he had the chance, thus restricting the value of the assistance John could provide them with- even the most detailed information wouldn't compare to actually being in the field and thus being able to explain what to do 'on-site', as it were-, but if he waited until the Wraith were nearly on them then Sumner wouldn't have much choice but to let John help them in a more active role.

"Taking part in this fight is really important to you, isn't it?" she said, looking thoughtfully at him.

"There's no question about me taking part in this; recent events just make it more important," John replied, his tone solemn as he looked back at her.

"Recent… you mean the fact that we've been able to dial Earth again?" Elizabeth repeated, looking at him in confusion. "But wouldn't that make it _easier_-?"

"You think the Wraith won't be interested in the possibilities opened up by regular access to the Milky Way galaxy?" John interjected, looking back at her with a solemn expression on his face.

Elizabeth's blood practically froze at the implications of that last comment.

She couldn't believe it; after all the time they'd spent trying to dial Earth from this end, it had never really occurred to them- beyond the obvious passing thought in the beginning when seeking an explanation for that 'quirk' of the program that controlled the gate shield; after a while they'd just focused on dealing with it rather than worrying about why it was there- that the shield hadn't been set up to keep _them _out of the Milky Way galaxy, but to keep the _Wraith _out.

Hell, John had _told _her that he'd set the shield up to stop the Wraith from getting to Earth, and she'd _still _not realised what he was saying; she was so focused on _them _being able to get back to Earth that she'd forgotten that they weren't the only race in the Pegasus Galaxy with an interest in that particular goal!

"But… but _how_?" she asked, looking in shock and confusion at John, only realising after she'd spoken that the question didn't make immediate sense; how would John know what she was asking him?

"The Wraith captured Captain… Gemmel, wasn't it?… when Sumner's team first went to Athos; from what Sumner said in his report, they were already beginning to torture the poor guy when Sumner arrived there and had to kill him," John explained, his expression grim as he looked at her, clearly having guessed what she meant by her last statement even before she could figure out a more appropriate way to phrase it. "The guy would have fought, I'm not denying that, but no matter how much he'd have guarded specific details about where he came from, the Wraith interrogating him _would _have picked up the basics at least; we _are _talking about a race with telepathic abilities, after all…"

He paused for a moment, staring at Elizabeth to make sure she understood what he was saying, before she finally finished what he'd told her.

"They know about Earth…" she said, her voice low as the horrific implications of that statement sunk in.

"Along with the fact that Atlantis is the only way to get there… and from Earth, pretty much every other planet in the Milky Way galaxy," John said grimly. "A whole fresh supply of food for the Wraith, of potentially limitless scale and growth, never having been a victim of a culling before…"

He stared pointedly at Elizabeth as he continued to speak, the grim expression on his face making the severity of what he had to say clear.

If Atlantis fell into the Wraiths' hands, _everything _was lost.

"I'll… I'll make sure we keep that in mind," Elizabeth said, wishing she could sound as assertive as she felt; the sheer scale of the responsibility she'd just found herself with wasn't exactly what she'd been expecting to deal with when she came here.

She was committed to doing what she could to protect the people of _this _galaxy from the Wraith, but that was mainly as more of a concept; they'd encountered so few people from this galaxy so far that there hadn't really been the opportunity to… _connect _with everyone here, really.

The Milky Way galaxy… for all that she'd only read about the civilisations the SGC had encountered in the reports she'd read during her brief period as head of Stargate Command… was more personal- more _real_ to her, almost- than those here; she had her home there, Earth had allies there…

She couldn't allow it to fall to the Wraith.

She _wouldn't_.

"We'll do everything we can, John," she said once again, nodding briefly at him before her expression changed to a more inquiring, slightly hopeful one. "On the topic of doing what we can, I don't suppose you could provide us with any further information about the satellite…?"

"Nothing beyond what the database can give you or what McKay just told you himself," John replied, shaking his head as he looked apologetically at her (Elizabeth knew that she should be more disturbed at the idea that he'd been watching that particular meeting, but by this point a little thing like that barely mattered to her; it just proved that she was right in thinking that he'd keep an eye on them until they needed him). "Given that I kept Atlantis at the bottom of the ocean ever since I first arrived in this galaxy, the odds of any Wraith weapons being able to affect the city at that depth were sufficiently low for me to feel comfortable relying on the natural defence of the ocean and my apparent absence rather than trying to repair the thing myself."

"Besides," he added, shrugging slightly apologetically, "I couldn't have actually done anything about it even if I'd wanted to."

"Really?" Elizabeth asked, looking at him with only a slight trace of anxiety about her expression at the implications of that last statement; he had _said _he didn't know anything they didn't know, but maybe they just hadn't reached something that he'd read himself yet. "Why not?"

"Well, given that the thing doesn't have any power- and hence has no life support or any means of activating the docking procedure-, I simply couldn't figure out a way to get into it to actually _do _anything," John said, shrugging in an almost nonchalant manner. "I could have extended the jumper's forcefield in order to create a basic 'tunnel' between the jumper and the satellite entrance to allow me to access it, but I still wouldn't have been able to do anything once I got there. The jumper's oxygen supply might have provided me with some kind of atmosphere, but it wouldn't be enough for me to actually carry out the kind of examination I'd need to figure out a way to get power on in the satellite itself, and assuming there'd been exterior damage I would have moving back and forth all the time…"

He shook his head dismissively. "It just seemed like too much effort to go into when planning for a situation that wouldn't actually cause _me _any trouble; the Wraith weren't going to do anything to the satellite so long as they thought it was useless, Atlantis would be safe enough so long as I kept it at the bottom of the ocean, and I knew that people would be here who _could_-"

He stopped speaking mid-sentence, a look of shock on his face as though he'd only just realised what he was saying, but it was too late.

* * *

"You _knew _that people would be coming here?" Elizabeth said, looking pointedly at him with an expressing that looked like she was trying hard to conceal a (admittedly justified, in John's opinion; he just hadn't felt comfortable bringing it up while he was still being hunted by Sumner's men) sense of betrayal. "How _could _you have-?"

"Look, that is a _really _long story, and I can't really tell you everything about it right now without you thinking that I'm insane," John said, his voice lowering slightly as he leaned in closer to look urgently at Elizabeth, placing his hands on his shoulders as he did so. "I'll tell you everything when I can; right now, all I _can _tell you is that I found something the Ancients left behind in preparation for someone coming to take up residence in the city when I first got here and tried to set up a home here with that in mind. It didn't give me anything beyond basic details about how to run this place- basically all the stuff you would have already learned back on Earth before you even came here in the first place- but I just got a few long-term tips about what to do keep things together until someone more professional came along…"

As his voice trailed off, his eyes fixed almost directly onto Elizabeth's, for a few moments he allowed himself to simply stare back at her, praying that she'd understand what he meant without asking for further details; he just wasn't _ready _to tell her about… _her_…

Finally, Elizabeth broke the seemingly tortured silence with a short, small smile.

"All right," she said, nodding briefly at him. "If you say you can't tell me everything now… so long as you've told me everything we _need _to know right now… I'll accept that."

"Really?" John said, allowing a smile of his own to reach his face.

"You've already saved this city at least three times; I think you've earned that much," Elizabeth said, before her expression became more serious as she looked at him. "Just so long as you _are _going to help us if those hive-ships get here… I can accept a _few_ little secrets…"

"Just don't make obvious I have them or that you're hiding that I have them, right?" John finished, smiling at her. "Don't worry about it; the second the reinforcements show up from Earth, I'll be dropping in to talk with Colonel Sumner and whoever else the SGC send to coordinate Atlantis's defences."

"Good," Elizabeth said, nodding back at him before she indicated the door behind them. "Well, I'd better get back to work; if nothing else, I need to give myself a little time before I mention my latest 'revelation' to Sumner…"

"Regarding what the Wraith want, huh?" John said, nodding in understanding.

* * *

"Of course," Elizabeth said, nodding back at him before she stepped back from the balcony, momentarily uncertain what she should say before she just decided to say it. "Well… see you later?"

"Count on it," John replied.

With that said, he turned around, placed one hand on the balcony, and swung himself over the side before releasing his grip, dropping down and out of sight even as Elizabeth looked at him, his black cloak the last thing she saw of him before he vanished from her vision.

If he had been any other man, Elizabeth would have hurried over to the balcony to see where he was going to hit the ground.

But it was _John_…

And somehow, for reasons even Elizabeth wasn't sure about, she knew that she could trust him to still be alive even after doing something like that.

Maybe it was a crazy action on her part, but…

She trusted him.

She had no real idea why at times- she knew so _little _about him when you got down to it, really- but she believed in him.

She just hoped that her faith in him wouldn't prove to be misplaced when the Wraith reached them…


	31. The Fate of the Satellite

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

"The Wraith are after Earth?" Sumner said, his expression grim as he looked at Elizabeth where he sat opposite her in the conference room the next morning; McKay and his small team had already left via puddle jumper for the satellite, but Elizabeth had gathered the remaining department heads to fill them in on her latest 'revelation'.

"They're after _access _to Earth, at any rate; if they can get access to our Stargate and its control crystal, dialling Earth from there would hardly be that difficult," Elizabeth explained, looking around at the rest of the people in the room while trying to give off an appearance of at least slight uncertainty; she had to look like she wasn't _certain _about what she was telling them in case they started to think she had been told this by someone rather than coming up with it on her own. "We already know that the Wraith have at least some psychic abilities; with that in mind, it seems likely that they acquired at least _some _information about Earth's location when they were interrogating Captain Gemmel."

"Couldn't the Wraith just be after Atlantis for the technology?" Lieutenant Ford put in, looking uncertainly at Elizabeth. "I mean, no offence meant, Doctor Weir- your theory's an interesting idea-, but there _is _some pretty impressive stuff here…"

"Most of which the Wraith are incapable of using due to their lack of the Ancient gene," Zelenka added, looking critically over at the young lieutenant. "Much of the technology that the Wraith might find useful is specifically encoded to render them incapable of so much as turning it on, and what is left is- from what we have been able to establish about their technological capabilities- nothing the Wraith would want or need. Doctor Weir's theory seems to be correct; the only real reason the Wraith have for coming here is to gain access to Earth."

"And from Earth, the rest of the Milky Way galaxy wouldn't be far behind…" Elizabeth said, her voice grim as she looked around at her staff. "We have to make sure the self-destruct is prepared if we have to resort to the worst-case-scenario; no matter what else happens, the Wraith _cannot _be allowed to gain access to that control crystal or the Milky Way addresses we've dialled so far."

"I'll see what I can do about adding the ZPM's explosive potential to the city's self-destruct sequence; even with what power we have left it should be enough to do a sufficient amount of damage to the tower to damage, if not outright destroy, the control crystal," Zelenka said, before his expression fell. "Unfortunately, that only covers what Atlantis can physically offer the Wraith; that still leaves the Ancient database."

"Is that not kept within the central spire as well?" Teyla asked, looking inquiringly at Zelenka.

"Not completely; the main databank is, but that is not the extent of the storage facilities used by the Ancients," Zelenka corrected, shaking his head as he glanced over at the Athosian before continuing. "The problem is that these systems are incredibly redundant; there are back-up systems located all over the city. Even with the most powerful explosive force we can offer, I cannot guarantee that we could destroy _all _of the database terminals to such an extent as to render the information inaccessible."

"All right…" Elizabeth said, taking a deep breath as she looked directly at her second-best scientist. "What's the alternative?"

"Delete the database," Zelenka said, his expression grim. "I cannot guarantee that such a thing would be possible in the amount of time- particularly since I would also be attempting to back up any information we can before leaving- but I will do what I can."

"Get to it as soon as possible," Elizabeth said, not bothering to hide the slight trace of regret on her face as she gave the order; it might be necessary to make this decision in order to prevent the Wraith gaining access to the information in question, but the idea of erasing all of the knowledge in the Ancient database was a decision Elizabeth was certain she'd regret having to make if they made it through this….

"Doctor Weir?" a voice said from outside the main door, prompting Elizabeth to glance up to see Chuck standing there, looking anxiously at her. "We just got a call from the gateship; Miller says they're nearly at the satellite and Doctor McKay's preparing to disembark and investigate."

Elizabeth couldn't help but smile slightly at this latest news.

Finally, something seemed to be going their way…

* * *

A couple of hours later, with no further news from the gateship beyond that they'd made contact with the satellite and McKay was working at restoring the power, Elizabeth was only partly surprised to look up while going over some papers to see Halling standing at the door, looking slightly uncertainly at her; even after all his time on Bates's offworld team, he still sometimes felt uncomfortable when the situation called for him to speak to her on his own.

"Halling?" Elizabeth asked, looking curiously at him.

"May we speak?" Halling responded, nodding slightly at her.

"Please, have a seat," Elizabeth replied, indicating the chair on the other side of her desk, Halling swiftly sitting down in it. "How is the evacuation on the mainland progressing?"

"My people will be ready," Halling said simply.

"Good," Elizabeth said, briefly noting and wondering about Halling's turn of phrase- should she be concerned that the Athosians who'd remained officially on offworld teams, such as Teyla and Halling, generally seemed to be coming to identify themselves with the expedition more than with their people- before he continued to speak.

"Doctor Weir," he said, his unease growing as he spoke- evidently he was uncomfortable with saying this but clearly felt that he should-, "word is there is a plan in place to destroy Atlantis."

"There _are _concerns that the Wraith will be able to make it to Earth if the city is left intact," Elizabeth admitted, not bothering to ask where Halling had learned that information- right now information relating to the approaching Wraith cruisers was the only thing anybody in Atlantis was even remotely interested in talking about-, "but I assure you that plan will only be executed in a worst-case scenario."

"Such as three hive-ships flying towards Atlantis?" Halling asked (Elizabeth had to admire the man before her, really; even when discussing something so deeply part of who he was- his belief in the Ancients' protection was fairly well-documented-, he continued to maintain his control).

"We do believe we'll be able to destroy them before they arrive," Elizabeth replied, taking care to avoid giving voice to her own feelings on this matter; she was just as strongly against destroying Atlantis as Halling was, but she was partly ashamed to admit that her reasons had almost as much to do with the fact that John would almost certainly be lost to her if that happened as they had to do with the knowledge of all the history and information that would be sacrificed if the city was destroyed…

"I understand you fearing for the well-being of your people," Halling continued, his tone continuing to be uncertain even as his voice remained clear and resolved, "but it is not reason to destroy the city of the ancestors. Atlantis is a sacred place, and to even consider destroying it merely for self-preservation-"

"'Merely for self-preservation'?" Elizabeth repeated, almost hurt that Halling believed they could be so selfish; they were trying to protect _everyone _back in their original galaxy from the Wraith, this wasn't just about keeping _themselves _safe!

"This place is all that remains of the greatest race ever to inhabit the stars-" Halling began.

"And you would prefer that it fell into the hands of the Wraith?" Elizabeth countered; she had been trying to maintain a respectful attitude towards Halling's beliefs, but his last comment had practically demanded a response on her part as far as she was concerned.

"I would have faith that the Ancestors- and the Phantom, of course- would not allow that to happen," Halling replied. "They have been able to preserve Atlantis for ten thousand years-"

"The Phantom told me _himself_ that he would rather this city be destroyed than allow it to fall into the Wraiths' hands, Halling," Elizabeth interjected; as much as she'd promised John that she would keep his contact with her secret, right now she felt that it was more important to reassure Halling that she wasn't completely disregarding the Athosians' opinions simply because she felt she knew 'better'.

Halling stared silently at her for a moment clearly contemplating what she had just said, before he spoke again.

"You claim to have spoken with the Phantom?" he asked, his eyes narrowed slightly as he looked at her.

Elizabeth didn't need diplomatic expertise to know what Halling's reaction meant; he thought that she was lying to him to try and convince him to accept her plan.

"I _have _seen him, Halling," she said, her mind latching onto the one thing she could think of that might convince him of her sincerity; the masks the Athosian children wore when playing as the Phantom covered the whole face, but that could just be because nobody could precisely copy the real thing… "The lower left side of his face is not covered by his mask, and the skin underneath it is pale."

For a moment, Halling simply stared silently at her, and then his eyes widened as he leaned in closer to her, his expression clearly stunned at this latest revelation.

"You have _spoken _to the Phantom?" he said, staring incredulously at her. "The secret of his mask is known only to the leaders of the people he trusts; all others only know that he wears a silver mask without knowing what it truly covers…"

"I have spoken to him, I promise you," Elizabeth replied, nodding back at the Athosian. "He has assured me that we shall have his protection as we fight the Wraith, but, if the situation becomes impossible, he assures me that the city can be sacrificed; no matter what else happens, he _will_ continue to protect the Pegasus Galaxy, and I can assure you that we'll do everything we can to help him."

For a moment, Halling sat in silence, looking contemplatively at Elizabeth, before he finally spoke.

"You have the approval of the Phantom," he said, his tone solemn as he looked at her, his gaze no less intent than it had been when he'd entered despite the shift the conversation had taken. "It is… comforting… to know that you have not made this decision without consultation."

"I'm glad you feel that way," Elizabeth replied, nodding gratefully back at him, understanding what he meant; since the Phantom had fought against the Wraith for the people of the Pegasus galaxy for the last twenty years, Halling evidently felt that the Phantom would not have agreed with Elizabeth's planned course of action unless he was certain that it was the only choice left to anyone. "But I can assure you, Halling, we will _not _abandon Atlantis to its destruction until we are certain there is no other choice; Jo- _the Phantom _has made it clear to me that he will only allow us to destroy the city if he is certain that every other alternative has been exhausted."

She was putting words into John's mouth, of course, but she felt that it was appropriate enough in this instance; he might have never voiced his opinion on whether or note Atlantis survive, but Elizabeth was certain that John would only allow Atlantis to fall if he was certain no other option was left to ensure that the Wraith failed.

"That is… reassuring, Doctor Weir," Halling said, smiling slightly at her before his expression became more solemn once again. "If only I could believe that such an action- should it be required to prevent the Wraith from claiming this city- would not almost certainly leave this galaxy without its greatest defence, I would support it completely."

Elizabeth could only stare silently after the Athosian as he stood up and walked out of her office.

She had to admit, it was hard to find a response to _that _one. Even if she was able to convince the SGC to continue sending ships and teams out to explore this part of the universe after the city was destroyed, the loss of the Ancient technology in Atlantis- to say nothing of the security they enjoyed in the city itself- would be a significant handicap to any attempts to establish an effective opposition to the Wraith, to say nothing of limiting their ability to fight back; they had enough trouble trying to find an Alpha Site in this galaxy, how were they meant to establish a _permanent _headquarters on another planet?

There were some days where Elizabeth _really _wished she'd gone with her initial feelings and told Vice-President Kinsey where he could go when she'd met him; even _before _she learned about his long-time vendetta with the SGC, she hadn't liked that man…

* * *

"Doctor Weir?" a voice said, knocking at her door. Glancing up, Elizabeth was relieved to see Zelenka standing there; at least _this _conversation was liable to leave her feeling less like she'd be condemning innocents to save herself.

"Yes, doctor?" she asked, looking back at him. "What progress have you made?"

"Well, the results so far are mixed," Zelenka replied, shaking his head apologetically at her. "The solution's simple enough- corrupt the Ancient database to make it unusable- but it's the _execution _of it that is proving to be difficult."

"You're creating a virus?" Elizabeth asked, looking inquiringly at him to make sure she understood what he was suggesting.

"Essentially, yes," Zelenka confirmed. "A plain old computer virus, once introduced into the system, wipes the database clean. It could be downloaded as part of the self destruct countdown; might even affect the Wraiths' systems if they try to access it."

Elizabeth had to confess, that last would be a nice bonus, but having a means of erasing the database didn't answer the most important question she wanted to know the answer to right now.

"How much of it could we save?" she asked, looking at the Czech scientist.

"I'm sorry?" Zelenka asked, looking curiously at her.

"Of the database," Elizabeth clarified. "Could we transfer the data through the Stargate back to Earth, maybe-?"

Zelenka instantly shook his head.

"It won't work," he said apologetically. "Putting aside the fact that the sheer size of the database would require more than ten times the amount of hard drives we brought with us, Ancient systems are too complex for us to download information of this scale directly into our own systems over wireless transmissions; we need time to write a program that can effectively translate the Ancient data into something that we can use, and even then it shall take some time before the process is complete."

Elizabeth didn't need to ask how long it would take for them to download all the available data even if they had enough hard drives available; Zelenka's expression made it clear that it would take longer than they had available to them right now.

Although she had never been the type to let her emotions rule her actions, Elizabeth couldn't help but swear at this latest turn of events.

If they had to leave Atlantis, they really _would _lose everything…

"You _have _to be able to save more than that!" she insisted, looking desperately at Zelenka; they couldn't have come this far only to come away with so little. "How can I be expected to choose between Zero Point Module research and their work on ascension? Between weapons schematics and their notes on space travel? No matter _what_ we choose here, invaluable information will be lost, and that's just what we've deciphered; we all know we've barely even _begun_ to scratch the surface. What if we destroy… the cure for all disease, or even some piece of information that could lead to the downfall of the Wraith?"

Zelenka could only shake his head apologetically.

"I don't know what I can tell you," he said regretfully. "I will try to improve on McKay's compression ratios, but we are at war, Elizabeth. In war, there are casualties."

Elizabeth knew that well enough; her long experience with drawing up treaties had made her more aware than any non-soldier had a right to be of the losses that could be suffered in war.

She just wished there was something _more _she could do right now…

* * *

A few hours later, Elizabeth could only stare in frustration at the paperwork before her, wishing she could concentrate enough to figure out what she could do to provide some kind of positive contribution to the mess Atlantis was currently facing. After Sumner's teams efforts to scout out a planet as a possible Alpha Site location had resulted in them being chased off by a life-form that- according to Ford- looked remarkably like a dinosaur, their list of possible Alpha Sites if the SGC reinforcements couldn't get here in time was diminishing rapidly, and they _still _didn't really have a clear plan for defending against the hive-ships with access to only one depleted ZPM…

"Doctor Weir?" Chuck's voice said from outside her office door, prompting her to glance up from her paperwork. "We just detected the hive-ships arriving in this solar system; they'll be at the satellite within the next few minutes. We're about to try and make contact with the gateship to determine what progress they've made; we thought you should be there when we reach them."

Simultaneously excited and afraid at this latest news- there was no way of knowing how McKay's small team had progressed in their attempts to activate the satellite, but if it had worked out they might have found a way to stop the hive-ships from even reaching Atlantis in the first place-, Elizabeth stood up and headed for the control room, nodding briefly at Chuck as he activated the communication system.

"Gateship, this is Doctor Weir," she said, taking care to keep her voice calm; no matter how worried she was about how things were turning out, she would _not _show fear. "How are things progressing?"

"_Doctor Weir, this is Gateship One_," Miller's voice replied, sounding as calm as could be expected under the circumstances. "_Doctor McKay has just finished routing the power to the satellite's weapon systems, and Doctor Gaul is inside the satellite; the satellite is currently powered down and we're waiting for the hive-ships to come into range before reactivating it_."

"Good call," Elizabeth said, trying to restrain the sigh of relief she felt at the news that the satellite was active; at least they had a _chance _to strike the first blow now. "Let us know when you're ready to fire."

"_Confirmed_," Miller replied briefly, the radio subsequently falling silent.

After a few moments with no further sound from the gateship, more and more people gathering within the control room as the news about this latest turn of events spread throughout the city, McKay's voice finally spoke again.

"_Doctor Weir_," he said, his voice grim as he spoke, "_it's McKay. _Satellite is armed and ready. It should fire within the next minute or so. Keep your fingers crossed."

"Fingers crossed," Elizabeth replied, nodding in response to his statement as she glanced around the room at the rest of her staff; she could even see Sumner, Teyla and Ford off to one side of the room, clearly waiting for news of their teammate's fate. "Good luck."

Once again the radio fell silent, the tension increasing as the group waited anxiously for news from the small ship that now served as their only hope to deliver damage before their enemies reached the city, before McKay's voice finally spoke once again, glee evident in his tone alone.

"_We have a kill_!" he yelled, prompting cheers and applause thoughout the control room, Elizabeth smiling in delight as she saw a couple of technicians enthusiastically hugging each other; even Sumner seemed to have developed a slight smile.

"We copy that, Rodney," she said at last, as the cheering stopped.

"_One down, two to go_!" McKay said, a broad grin somehow apparent even across the vast distances between them as the radio fell silent once again.

For a few moments, the atmosphere in the room was charged and energised, each member of the expedition eagerly awaiting the now-seemingly-inevitable news that the satellite had destroyed another hive-ship, that they wouldn't even need the reinforcements from Earth for this first wave, that they'd saved the city by themselves…

Then McKay's voice broke the silence, his tone alone once again saying everything that needed to be said even before he spoke. "_Atlantis, this is McKay. We have lost the satellite_."

The sudden shift in mood in the control room was almost painful for Elizabeth to witness.

"Did you manage to take out any more ships?" she asked finally, deciding to address the central issue before any further questions were asked.

"_Negative_," McKay replied. "_Two of the hive ships are intact_." There was another brief pause, as though what he was about to say was especially painful for him, before he spoke again. "_Elizabeth… Brendan Gaul was aboard the satellite_."

_The first casualty of the siege of Atlantis…_ Elizabeth replied, saddened at the news of that bright young doctor's future cut short so rapidly by forces so powerful that they would probably never even acknowledge his existence as a person.

"Understood," she said, bringing her attention back to the present; they would mourn Gaul once they had time. "What's thes tatus of the other two?"

"_They're not coming any closer_," McKay replied, the news providing so little encouragement that nobody so much as smiled at it. "_Looks like they're rethinking their plans. At the very least, he's bought us some time_."

"You can't do any more out there, Rodney," Elizabeth told him, fighting to stop herself breaking down at this newest turn of events.

She hadn't realised how much she'd been counting on that satellite until it had failed them…

"Return to Atlantis," she finished,

"_On our way_," McKay replied, terminating the radio and leaving the control room in silence.

_This is it…_ Elizabeth mused as she looked at the people around her, nodding slightly in recognition of the resolve she saw on their faces. _Our first line of defence has fallen… reinforcements might not be here in time… and our only hope to hold the line on our own lies in a power source that only has access to just over a tenth of its full power available to it and a man whose origins are a complete mystery even to _me_…_

She paused at that last thought.

_Hold on…_ she thought. _Why do I feel like I _should _know more about him? He's only spoken to me because he knows I won't hand him over to Sumner; why should I feel as though he should have told me more than he already has_…?

She shook the thought off impatiently; it wasn't going to help her deal with the current situation to start thinking about what the Phantom should or shouldn't tell her… not to mention wondering why he felt as though he _should _have told her more than he had so far.

"Doctor Zelenka," she said, turning to look grimly at the Czech scientist, "make sure that virus is ready to be uploaded if we need it."

With that said, she turned to address the rest of the people in the control room, raising her voice to make sure that everyone in the room could hear what she was about to say.

"All right then, everyone," she said, her expression grim as she looked at the group now gathered before her, representing many of the expedition's senior members and division leaders, "we have only hours left for certain before those hive-ships reach here; everyone return to your respective groups and inform them to prepare for possible invasion. I want the control chair ready for use as soon as possible and all possible defensive systems ready to fire the moment those hive ships reach us; we might only have a few dozen drones, but we are going to make _sure _that those shots _count_."

She paused for a moment, making sure that she had everyone's attention before she spoke her final words.

"We came to this city to learn from the most advanced race ever to exist," she said simply, her arms folded as she looked at the people around her. "We are _not _going to let a race of alien vampires take it away from us without a fight."

With one last nod of acknowledgement at her people, Elizabeth couldn't help but allow herself a slight smile as everyone turned to begin their appointed tasks.

_Here goes nothing_…

* * *

Up in the maintenance tunnels above the control room, crouched low on the ground as he studied the sight before him, John allowed himself a slight smile as he looked at Elizabeth issuing instructions to the people around her.

She was right about one thing; the Wraith would _not _take Atlantis without a fight.

All he had to do now was to make sure he did everything he could to make the fight more even in _their_ favour, rather than favouring the Wraith.

_Which means_, John mused to himself, a grim expression underneath his mask, _that I'll soon have to make contact with Sumner_…

The trick here was going to be to make contact at the right moment…


	32. Come Together

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

In many ways, Elizabeth wasn't entirely certain how to feel when the Stargate activated and Earth's IDC was received from the other end of the wormhole, shortly after McKay's Gateship had returned to Atlantis with its two remaining passengers.

On the one hand, the concept of reinforcements arriving for them at a time like this was certainly welcome; even with the two days McKay's actions with the satellite seemed to have brought them- the remaining two hive-ships had significantly slowed their progress towards Atlantis, most likely now uncertain what the city might have to offer in the way of defences-, their options for defence were limited to just the few dozen drones remaining in the city's weapons' storage and whatever power remained in the shield, and Sumner and McKay had both hade it clear that they doubted they possessed the necessary power to run the shield for more than a matter of hours under sustained assault.

If they were going to hold their own in this kind of situation they would definitely need far more trained soldiers than they had at present; in this kind of situation, any kind of aid would unquestionably be helpful.

On the other…

She was almost ashamed to admit it, but, in some way, she'd wanted to _prove _herself capable of defending the city on her own without anyone else coming in. She and the expedition had made this city their own since arriving in it almost a year ago; on some level, she'd wanted to prove that they deserved to be there by being the ones to save the city themselves, without the aid or assistance of anyone else.

_Oh well_, she reflected silently, hurrying down the stairs to greet the new arrivals- Ford already at the bottom and saluting the man standing before him, she noted-, large crates accompanying the new arrivals through the wormhole. _You can't always get what you want, and at least this is a _positive _change…_

"Doctor Weir," the man Ford had just been saluting said as he turned to look at her, revealing a weathered face with short, curly pepper-coloured hair and a high forehead, before he looked past her to smile at Colonel Sumner. "Marshall."

"Dillon?" Sumner replied, a smile crossing his face as he looked at the other man. "Good to see you, old friend; we could use all the help we could _get _right now."

"I gathered," the man replied, the slight smile he shot in Sumner's direction making it clear he intended no slight towards Sumner with that statement before he turned back to look at Elizabeth, a grimmer expression on his face. "Colonel Dillon Everett, United States Marine Corps; General O'Neill sends his compliments on a job well done under extraordinary circumstances, but as of now Atlantis is under our command; you are relieved."

Elizabeth blinked.

She'd been prepared to accept that they'd have assistance in saving the city from the Wraith, but to be informed that she wouldn't even have a say in the defence of the city she'd been leading for the last year…

"Excuse me, Colonel," she said, stepping forward slightly to look the new arrival directly in the eye- after staring down Kolya during the siege, she'd be _damned_ if she'd back down from somebody who was officially on her side-, "I don't think you fully grasp our situation here-"

"You have have three Wraith hive ships bearing down on your position and precious little to defend yourselves with," Everett interjected, looking at her as though she was a child who refused to leave the adults to do the talking. "That about sum it up?"

"It's actually down to two hive ships now, Dillon," Sumner put in, looking slightly apologetically at this man (Whom Elizabeth was increasingly certain Sumner had already known before this meeting). "We've managed to destroy one already, but as stated in our message our power reserves are limited; right now we're limited to just a few dozen drone weapons and maybe a few hours of protection from the shield if the Wraith start firing at us with everything they've got."

"Yeah, I heard about that; you never give me the easy ones, do you, Marshall?" Everett replied, shooting a briefly joking smile at the man Elizabeth was increasingly convinced was an old friend of his before he became more serious once again. "Still, we've got the ZPM from Egypt being transported up to _Daedalus _even as we speak; all we need to do is hold the line here until they arrival. Marshall, I'd appreciate it if you could fill me in on our tactical situation here as soon as possible; I need to know how to distribute my men as soon as possible."

"Trust me, Dillon, right now _any _men you can bring would be a help," Sumner said, nodding at his friend before the two of them began to walk up the stairs towards the conference room, Ford and a group of the newly-arrived marines behind them, none of the soldiers even bothering to let Elizabeth or McKay know they could come along as well.

"Colonel Everett!" Elizabeth yelled, looking pointedly up at the two colonels as they turned around to look back at her. "Fine, you're in charge. But I should be at that briefing."

"Doctor Weir," Sumner said, looking over at her, "when it comes to Atlantis's general operations, I respect your decisions, but this is a military matter; your presence is not required at this time."

"I understand that-" Elizabeth began.

"Good to know," Sumner interjected, unaware or unconcerned- Elizabeth wasn't sure which was worse- that she'd had more to say, before he and Everett continued on their way towards the conference room, evidently regarding the matter as closed.

Elizabeth could only stare in stunned silence at the stairs where she had just been so casually dismissed from the meeting that could decide the future of the city she had come to call home.

_So much for bonding with people_… she reflected bitterly to herself; even after everything they'd been through since arriving here, Sumner evidently still regarded her as little more than a paper-pushing politician, capable of making diplomatic decisions but unable to cope when the time came for hard military action.

Sighing in frustration, she turned around and walked up the stairs towards her office, unaware of the silent figure clad in black that was watching her from an observation hatch he'd set up in the tunnels he used to get around the city, one fist clenched resolutely before he turned around and began to crawl along the tunnel towards his destination.

* * *

"This schematic is based on the information we got in your original message," Everett explained as he spread out a large piece of paper on the conference table, looking curiously at Sumner and Ford as he spoke.

"I take it nothing else has been discovered that might impact any plans?"

"Unless you've recently changed strategies since I last saw you, not likely," Sumner replied, shaking his head with a slight smile. "What did you bring?"

"Given what you said about your drone weapon shortage, the SGC thought it best to provide further weapons for Atlantis, so we've been provided with some of the rail guns that were due to be added to _Prometheus _during their next refit," Everett clarified, a slightly satisfied smile on his face as he spoke. "They'll deliver an impact velocity of mach-five at fifty miles; a standard magazine will hold ten thousand rounds."

"_Nice_," Sumner reflected, nodding in approval. "Good call…"

Further conversation was cut off as Doctor Weir walked into the room, looking pointedly at the two colonels before her as they turned around to look at the new arrival.

"Doctor Weir?" Sumner asked, looking uncertainly at her. "Is there something you want us to clarify?"

"Start with everything and work your way up from there," Doctor Weir replied, her arms folded as she glared at the two men. "Colonel Sumner, I have spent a year in command of this facility and you have never before questioned me when it comes to command decisions-"

"With all due respect, Doctor Weir," Sumner countered, glaring pointedly back at her, "that was when we were organising exploration and recon missions; this is a strictly military matter-"

"Concerning the lives of everyone on this base, whom I have personally been responsible for, both military and civilian, for the past several months," Elizabeth interjected; she was beginning to feel increasingly like she was talking to herself with the amount of progress she was making with this situation. "I am _not _about to put those lives in jeopardy until I at least know how you intend to defend this city."

"I don't need to explain myself to you, Doctor," Everett responded, his tone as cold as though he was talking to an enemy soldier who'd asked an impertinent question rather than someone who was meant to be his equal. "And I don't need your cooperation."

"But you could _probably _use mine," a voice said from behind them.

Spinning around, the two colonels and their respective men were shocked to see the new arrival. Standing casually behind the monitor that was currently displaying Atlantis and the distance the hive-ships had yet to travel, his arms casually folded as though he was merely there having a chat with some friends rather than in a room full of people who'd want to capture him, stood the Phantom, smiling slightly nonchalantly underneath his silver mask.

"_You_?" Sumner yelled, staring incredulously at the man before him.

"Me," the Phantom replied, his narrowed eyes underneath his mask the only hint of emotion. "And I'm here to make a deal; keep Doctor Weir and the Athosians in the loop while arranging the defence of Atlantis, and I'll offer you my assistance in exchange."

* * *

For a moment there was silence as the expedition's leaders tried to process what they had just learned- Sumner and Everett confused at the terms while Elizabeth was left wondering why John would take such a risk for something so personal-, before it was broken again.

"Excuse me?" Everett said at last, looking sceptically at the man before him as he walked forward a coupe of feet so that he was more directly facing the new arrival. "You'll help us if we keep Doctor Weir informed? Why?"

"For the simple reason that she is the only one of you three whom I trust not to arrange to stab me in the back- metaphorically, anyway; I freely acknowledge that nobody here _would _stab me in the back, you'd just stick me in a cell somewhere and try and make me talk-, and, therefore, I would prefer her to actually have some _say_ in what happens here," the Phantom replied, his tone continuing to sound frustratingly casual as he looked at the people around him despite the fact that all of them had guns at their sides and he appeared currently unarmed.

"And what guarantee do we have that you'd be honest under those circumstances?" Everett countered.

"My word," the Phantom replied simply.

"The word of a man in a cloak and a mask; forgive me if I'm not exactly reassured," Everett retorted, continuing to glare as he spoke. "What's to stop us just doing what you said originally and-"

Before he could finish the next word, the Phantom had unfolded his arms, drawn an energy pistol of some kind, and then proceeded to shoot the guns of all the soldiers before him out of their holsters- while avoiding causing any actual damage to the guns or the men carrying them- before apparently closing the conference room doors with nothing more than a flick of his hand.

"Because if I wanted to take control of this city for myself, it would be _that _easy; the fact that I haven't done that suggest that I actually _am _interested in working with you?" the Phantom asked, a slight smile under his mask as he took in Everett's stunned expression at the Phantom's nonchalant attitude at what he had just done before the expression under the mask reverted to its original neutral look. "We're _all _going to be in trouble when those Wraith ships get here, and I've been fighting the Wraith- both one-on-one and in their ships- for the better part of the last decade or so; can you _honestly _say you couldn't use that kind of expertise?"

After another brief, tense stand-off, Everett sighed and nodded.

"All _right_," he said, everything about his appearance making it clear that he wasn't happy with this arrangement but recognising that he had no other choice. "What do you _want_, exactly?"

"Oh, it's simple enough; just to know that you'll give _everyone _in this city an equal role in its defence, that you'll listen to what I have to tell you about Wraith tactics… that kind of thing, you know," the Phantom said, shrugging slightly before he raised one hand. "Deal?"

"…Deal," Everett said; he wasn't happy about it, but the simple acceptance was all that the Phantom needed right now.

"Good," he said, waving one hand to open the conference room doors once again. "So, what did you _bring _here to help us deal with these assholes?"

Glancing around at his men, each of whom were already now holding their weapons after picking them up from where they'd fallen, Everett momentarily allowed himself to entertain the possibility of trying to _make _the Phantom tell them what they wanted to know on _their _terms- he just wasn't… comfortable… relying on someone like the Phantom; the man was an irreverent vigilante with no apparent moral code regarding treatment of prisoners or cooperation with others-, but then he remembered how rapidly the Phantom had disarmed his men and decided against it; starting a firefight wouldn't accomplish anything right now and would probably only end badly for him anyway.

The only thing he _could _do was try and give the Phantom just enough leeway to be of assistance while making sure to wait for an opportunity to take him by surprise as soon as he dropped his guard; this man was _far _too dangerous and independent to be allowed to remain the loose cannon that he was at a time when they were at war…

* * *

"Right then," the Phantom said, clapping his hands together sharply as he looked around the room at the soldiers gathered before him, a slight smile on his face as though his earlier actions had never happened, "aside from the rail-guns and a few dozen drones, what else did you bring?"

"Six naquadah-enhanced nuclear warheads, twelve hundred megatons apiece," Everett answered, almost operating on automatic; what was important now, as far as he was concerned, was remaining patient until the time was right. "They emit almost zero EM and are otherwise invisible to radar. Once deployed, they will detonate by proximity fuse-"

"Keep about half of them back just in case," the Phantom interjected.

"Excuse me?" Sumner asked.

"The Wraith have this nasty habit of setting up seemingly natural disasters to catch you off-guard when dealing with the more advanced races out here, and their own sensors are _very _advanced into the bargain," the Phantom clarified, looking pointedly at Sumner. "Deploy two or three, I'm not objecting to that- we could use every advantage we can get at this point, and they should stop the asteroids if nothing else-, but if we put everything we've got out there at once, we're _never _going to win."

Everett wasn't sure what frustrated him more; the fact that the Phantom was _already _telling him how to do his job, or the fact that what he was saying actually made sense.

"Right…" he said, trying to regain some sense of control as he looked resolutely at the Phantom. "I understand from the files that you've displayed the ability to control these 'puddle jumpers' by remote from the chair?"

"How- oh yeah, that incident with the… Iratus bug, right?" the Phantom said, clicking his fingers as he remembered the incident in question. "Oh yeah, I can do _that_; just don't ask me to teach anyone how to do it themselves."

"Excuse me-" Sumner began, looking in frustration at the Phantom.

"Look, the control I need to do that without blowing up the jumper by giving a drone too much power is _ridiculously _focused; it took me over a month to be certain I could do it without blowing the ship up by trying to take it on a flight of longer than a few metres, and that was when I had nothing to worry about but _myself_," the Phantom said, looking around in frustration at the two colonels. "I can give your men flying lessons, but the fact remains that I'm the only one who can do some stuff, and even that's only because I've had a lot of time to practise; at the end of the day, I'm your best candidate when it comes to some of the trickier things like getting the control chair working."

"On that topic," Elizabeth said, stepping forward slightly as she moved to address the Phantom- if she was going to be allowed to participate in this she was _going _to make an active contribution-, "I assume we can count on you to operate the control chair when the time comes?"

"Control chair?" the Phantom repeated, turning to look at her with a brief smile. "Oh yeah, that's easy enough; I couldn't do _much _practising with firing drones underwater- didn't want to waste them needlessly-, but I've managed to get the chair to do everything else I wanted it to do without any problems."

He glanced back over at Sumner as he saw the man opening his mouth. "And before you ask, the chair as a whole is _another_ system you need to practise using quite a bit before you've got it working properly; if you don't know precisely what you're doing in a tense situation you run the risk of making things worse the moment you sit down in that thing."

"So, in other words, according to _you_, you're the only one who can effectively get this city to do about half the things it's capable of doing?" Sumner asked, looking pointedly at the Phantom.

"The only one who can do them in the time frame we _have_, Colonel Sumner," the Phantom clarified, raising a hand as he returned Sumner's glare with one of his own. "If we had more time before those hives get here I could maybe train a few people to do what I can do, but that's about it in this kind of time frame; you let me do it, or we're all dead."

Everett didn't like this; it seemed like their entire hope of survival depended far too much on one figure they knew little to nothing about in terms of his past _and _his motivations, with only a few legends from a bunch of primitive hut-dwellers in various parts of this galaxy to give them any kind of 'proof' that he wasn't going to turn on them at a moment's notice…

But then he remembered General O'Neill's orders to him before moving out- "_Work _with _the Phantom if you run into him; guy sounds like we want him _with _us rather than hacking him off by trying to lock him up_"- and he knew that, in the end, one thing the Phantom had said was the truth; they needed him.

If _anyone _was going to get out of this alive…

They needed the best man available to make the control chair work, and right now all the evidence they had made it clear that the Phantom could make Atlantis do things the rest of them couldn't even _begin _to attempt at this point…

Everett swore under his breath.

He _hated _it when he had to work with loose cannons like this masked lunatic…

He just hoped that it wouldn't come back to bite him in the ass in the not-too-distant future…


	33. First Failure

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

As John sat in the co-pilot seat of the jumper- he might call it a gateship for the sake of the others but he would _always _think of it as a puddle jumper-, casually giving a few quick pointers to some of the new 'gateship pilots'- as everyone else referred to them-, he couldn't help but feel a bit wistful at how things had turned out since he'd made contact with the colonels only the day before.

Neither of them were exactly _happy _that he'd just dropped into their lives like this, of course- his fingers kept on drifting towards the gun he still wore underneath his cloak every time he turned his back on one general or another, his senses constantly alert for any sign that anyone was going to try something that they shouldn't-, but as he'd pointed out, they didn't have much choice but to accept his presence; he _was _the person best qualified to use the Ancient technology that they needed to defend themselves.

Right now, John was mainly just grateful that they were listening to his requests and had permitted Elizabeth to remain in a position of authority; his request might have been at least partly motivated by a desire to ensure she kept the position she'd worked so hard to make her own, but at the same time it was good to have someone in command that he knew was on his side…

"So… that's it?" the pilot- one of the new ones Everett had only just brought with him to Atlantis; he hadn't managed to pick up the guy's name yet- asked, looking uncertainly at the masked man off sitting alongside him.

"Yeah, that should be enough practise for the moment," John confirmed, smiling slightly at the man as he briefly went over the recent lesson in his mind; they'd covered most of the essentials on how to manoeuvre the craft, and the man had shown a certain creative aptitude for it that could be useful in helping him teach others, but in the end he was limited by the strength of the man's ATA gene…

_Ah well_, he reflected, as the man turned around to head back towards Atlantis- John spared a few moments to confirm that the men he'd been advising over the radio were still following him before they continued on their way-, _at least they're picking up the essentials_.

He just hoped that the extra weapons they were installing would be enough to turn the tide if the darts came in too close; with the ZPM down to only around fourteen percent- and he strongly doubted he had the time to convince Sumner and Everett to let him go and recover some extras from his ZPM stockpile; given the distance he'd need to travel via jumper to reach his 'storeroom' even after going through the 'gate, they'd probably be more inclined to think that he was trying to run away rather than help them- he _really _wasn't that keen on activating the shield and losing that power until he had absolutely no option left to him…

* * *

"So," the Phantom said as he stood at the top of the conference table- looking back, Sumner wasn't entirely sure _how _they'd ended up with this masked man in a position of authority in these matters, but somehow he just wasn't able to actually _do _anything about it-, studying the layout of the city before him, "we've got those railguns you brought stationed around these areas, capable of basically firing a hell of a lot of bullets at a very rapid rate once the targets are within visual range, correct?"

"Yeah…" Ford said, nodding at the man before him, his stance making it clear to anyone with any degree of military knowledge that he was just waiting for a chance to hit the man before him.

"Useless when the shields are up, I hope you realise; it's programmed to allow ju-_gateships _through easily, but nothing else can enter or exit the city once that shield's activated," the Phantom continued, looking up at the colonels before him before a slight smile appeared on his face. "Other than that, once the darts get in close enough the guns should be enough to handle them; with the population of the city concentrated in these central areas the Wraith would probably prefer to focus their attention on gaining access to the central tower as rapidly as possible… I think."

Everett blinked.

"You 'think'?" he repeated, turning to look pointedly at the Phantom.

"Well, it's not like I've had to defend _Atlantis_ fairly often; I always kept it underwater before now, and whenever I was helping to protect other cities I was mainly relying on their natural defences to provide shelter," the Phantom clarified, looking back at Everett with an equally critical stare. "I'm trying to adapt my tactics, but even with superior technology available to us here you have to take into account that Atlantis being on the ocean _does _limit the advantages offered by natural terrain…"

Everett could only glare back at the Phantom in frustration before he began to speak again, addressing Elizabeth, evidently recognising that he couldn't go any further with that line of questioning because he couldn't come up with an effective comeback for it; the Phantom's comment about the tactical disadvantage _was _an accurate one.

"We've deployed the warheads just as… the Phantom… suggested; half above us and half awaiting deployment pending later developments," the new colonel said, waiting a moment as though hoping that Elizabeth Weir would tell him to deploy the other warheads like he clearly wanted to- with being kept 'in the loop' she could technically retain the authority to counteract the Phantom's 'orders'- before he continued. "Unfortunately, given our limited drone supply, attacking the hive ships long-range is currently not an option at this point; I was thinking that the Phantom could help our pilots-"

"Find the weak points on the hive and tell you where to shoot?" the Phantom finished, sighing slightly as he looked back over at Everett. "It's not as simple as that, Colonel; did you miss the part where I told you that hive-ships are at least partly _organic_?"

"So?" Sumner asked, looking critically back at the Phantom.

"So, are you _honestly _telling me that if I hit you both in the same part of the body with the same amount of force, you'd both react _exactly _the same way to the damage?" the Phantom pointed out, his arms folded as he glared over at the two colonels. "Hive-ships are living beings, and thus their weak and strong areas vary from ship to ship; they might share some essential similarities, but even without taking individual 'training'- for lack of a better term- into account, the damn things have practically _evolved _so that those areas are well-protected, even if they're not always protected to the same extent. It's not always as straightforward as pointing a gun at a certain location and firing there; you've got to get used to quickly assessing where to hit to cause the maximum amount of damage with the minimum amount of firepower, and in this case there's just not time to show you where to aim in the time available to us."

"Which leaves us with the nukes as our best bet to take out the ships before they get too close," Everett concluded, nodding briefly as though the Phantom had just confirmed what he'd already known before he glanced over at Sumner. "In the meantime, it would probably be best to prepare our shorter-range defences in case some darts manage to get through; Colonel Sumner and I have already established rail guns around Atlantis in the event that those 'Dart' ships get in close enough to pose a threat."

"And, as I said, it's a good call so long as we only use them when the shield isn't active, otherwise we run the risk of shooting _ourselves _with the damn things from the potential ricochet; I'm not certain how the shield would react to _bullets _being used against it from the inside," the Phantom added, before a thought occurred to him and he glanced pointedly at the two generals. "Don't forget to deploy the Athosians around the guns to act as protection; they might not be able to operate the things to the same extent as the marines, but anyone here will tell you that the Athosians are _very _good at the hand-to-hand thing."

Once again, Everett's expression made it clear that he didn't like the Phantom's advice- like the Phantom himself, Everett clearly saw the Athosians as untrained amateurs interfering with the professionals-, but, with no real means of voicing his opinion without risking losing the Phantom's assistance when he needed it most, he simply nodded in acceptance of the suggestion.

Before anything further could be said, an alarm suddenly sounded throughout the city, prompting the four commanders to exchange puzzled glances before Chuck ran into the room, looking anxiously at the group around him before his eyes settled on Elizabeth (A fact that she couldn't help but feel slightly satisfied about; even in a military situation, the members of the expedition looked to tell _her _what was wrong rather than anyone else).

"We have incoming," he said, clearly shaken at this latest turn of events (Not that there hadn't been a great deal going on the last few hours to put him in that state; the reaction to the news that the Phantom was taking a command role during this siege alone had raised quite a few surprises when it had first been announced to the general population of the city). "I don't know where they came from; they just… _appeared_ all of a sudden!"

"How many?" Everett asked urgently.

"Hundred plus," Chuck said, shaking his head in confusion as he looked at Elizabeth. "I swear, I don't know _how _we missed them-"

"Because the sensors didn't register them as a threat until now," the Phantom clarified, shaking his head slightly as he looked over at Everett in frustration. "These aren't Wraith ships we've got coming for us; don't you remember what I told you about asteroids?"

"You said the Wraith triggered events that looked like natural disasters-" Sumner began.

"By which I meant meteor storms; what did you _think _I meant, that the Wraith would send something through the Stargate to trigger an earthquake or something like that?" the Phantom countered, shaking his head in frustration as he looked back at the screen; even as they'd been speaking the mines and the asteroids had both vanished from the screen, the mines detonating to leave nothing behind but residual radiation that.

"Well," the Phantom said after a moment's silence, Everett and Sumner briefly stunned into silence at their first line of defence being eliminated so casually, "that's one way to get the job done, I suppose."

"You _knew _that would happen?" Everett asked, looking in frustration at the masked man.

"In my defence, I _did _tell you that the nukes wouldn't work, I just wasn't expecting them to try _that_; plus, I wasn't certain how Ancient sensors would cope with that kind of radiation," the Phantom clarified, looking over slightly apologetically at the two colonels. "Of course, I admit I wasn't expecting them to actually unleash the asteroids _this _early- I must have given them more reason to be concerned about Ancient technology than even I'd expected-, but on the bright side, the bombs you _did _plant took all of the asteroids out before they reached us, and we've still got half of them to take out the hive-ships-"

"And how are we meant to get them _up _there?" Sumner cut in, looking over in frustration at the Phantom. "We're dealing with _bombs_, not missiles, and if you seriously think we're going to commit suicide to take them up in gateships based on _your _plans-"

"Actually, I was intending to send a couple of gateships up cloaked and under remote control from the chair; would that work out better for you, Colonel?" the Phantom interjected, his arms folded as he glared at Sumner with an expression of frustration that Elizabeth had long grown used to seeing on the faces of people who were dealing with McKay; wondering how someone who was allegedly so smart could be so stupid.

"And that'll work?" Sumner asked, looking inquiringly at the Phantom.

"We've still got around thirteen percent power in the ZPM even after all the testing I've been doing for you; it'll suffice," the Phantom said casually, before he glanced back at Everett. "You say the _Daedalus _should be here in the next couple of days?"

"Based on estimations of its speed when powered by a ZPM, all our engineers are fairly certain of it; you just need to allow for leeway given that the ship's never tried travelling _this _far before," Everett confirmed.

"Fair enough," the Phantom confirmed. "So, with that in mind, all we need to do is get the hive-ships in range and wear down the darts; given our relatively limited drone supply, I'd rather not use them until we _know _we're going to hit our target."

"The last time I checked those things were pretty accurate-" Everett put in.

"And the 'shields' of the hive-ships consist of the darts flying around them to intercept anything that might pack a big enough punch to damage the ship; do you really think that I can afford to release all of the drones we have left against _those _kind of odds?" the Phantom pointed out, shaking his head in frustration. "We've got _more _drones stored in Atlantis than we'd have in the jum- the _gateships_, but we still don't have enough to _completely _get through all the darts they'd be using against us, and there's no way I can maintain the fine control necessary to get a drone to the hive's weak spot in a combat situation like this…"

He shrugged helplessly. "Sorry, but with the way things are we're just going to have to partly bluff about the power we've got available to us if we want to get the Wraith to back off… and talking of which, I _think _we need to make sure your pilots and gunners are ready; after a show like _that_, the Wraith are going to want to come in as swiftly as possible while the radiation's still clouding our sensors."

Everett couldn't help but curse slightly at the realisation that the Phantom's comment was right; once again, the amateur had noticed what none of the trained professionals had.

Even the excuse that none of them were used to this kind of fighting- when the SGC had started out exploring the universe they'd been limited to more hit-and-run tactics rather than risking directly confronting spaceships, and even after they'd acquired the technology to build ships they'd tended to engage in ship-to-ship fights rather than trying to fight off ships from the ground- didn't excuse the fact that blocking an enemy's sensors to give your forces a chance to strike unexpected was an _obvious _strategy…

* * *

An hour or so later, their men all waiting at their relevant posts for the necessary call to action even as the Wraith appeared determined to outwait them, Sumner and Everett found themselves standing in the holographic information room, the Phantom standing behind the control podium for the room as he looked grimly at the two of them.

"You're sure you want to do this?" he asked, raising an eyebrow that was only just visible behind his mask (Sumner wished he'd take the damn thing off; how could you trust a man who wouldn't show you his face?). "It's not going to give you anything useful…"

"We'll be the judge of what's useful in this situation, Phantom," Everett said simply, looking pointedly at the man before him. "Show us what we want to see."

"If you insist," the Phantom replied, nodding briefly before he placed his hands on the console, causing the room's doors to close and its lights to dim before a vast blue-tinted hologram of what the colonels could only assume was the Pegasus galaxy- having never looked in detail at the stellar maps of this area neither of them could be sure- appeared above them.

"This is the status of the Pegasus galaxy before the Ancients encountered the Wraith," the Phantom said simply, looking at the two men before him as he spoke, clearly recounting a tale that he himself had already studied; the '_I told you so_' wasn't explicit in his tone, but both colonels knew that it was there nevertheless. "The blue stars represent systems either inhabited by or protected by the Ancients. Then…"

He briefly returned his attention to the controls, and a wave of red began to spread out across the stars, beginning in one corner of the galaxy before it rapidly "This is how it looked after they fought for almost a hundred years."

"Until Atlantis was all that was left…" Everett muttered as he stared at the hologram above him.

"Quite," the Phantom said, before the hologram shifted to focus on one specific solar system, subsequently moving to bring the focus on one specific planet in that system that Sumner and Everett didn't need to be told was the planet they now inhabited.

"That's when the siege began," the Phantom continued, as the holographic planet displayed multiple Wraith ships converging around the world before them. "For several more years, the Atlanteans were able to hold off their attackers thanks to the city shield and superior weaponry- the weapon satellite system was really rather useful in that regard-, but the central problem of numbers remained; no matter how many Wraith ships they destroyed, more kept coming. They could win almost every battle, but they saw no way to win the war. So, they submerged the city, and left."

With that, the Phantom terminated the hologram, the lights coming up once again as he looked pointedly at the people before him. "You can't deny that they paint a pretty clear picture of our situation."

"You think this is a no-win scenario," Everett said simply.

"What I _think _is that they're going to come back even if we beat them," the Phantom clarified, looking pointedly back at them. "I don't believe in the no-win scenario myself, but this is one of those cases where the only way to win this fight is to _not _fight."

"From what we've heard you've been fighting them for over a decade-" Sumner began.

"And I've survived this long because I used hit-and-run tactics and only attacked them on a large scale when I could be sure I wouldn't leave any survivors," the Phantom countered, leaning slightly over the control podium to glare at Sumner. "Your men went into that Wraith hive-ship with virtually all guns blazing and no real idea _what _you'd find, and then you ended up with that Keeper interrogating Captain Gemmel-"

"Which we wouldn't have had to deal with in the _first _place if you'd just told us-" Sumner began.

"I've been on my own here for twenty years; do you really think I'd have lived this long if I was _that _willing to trust everyone I met?" the Phantom countered, a slightly bitter tone in his voice as though the current topic was particularly personal to him. "This is a dangerous galaxy we're living in, Colonel Sumner; if I started out assuming that everyone I met was going to be nice to me I'd probably have been _dead _long before any of you got here."

"You still should have contacted us once we knew what we were dealing with," Sumner countered, wishing he could come up with a better comeback.

The worst part was that he actually _understood_ where the other man was coming from all too well; no matter how much he wished he could see a way to demonstrate the danger he knew would result from the Phantom's independent attitude and refusal to participate in the chain of command, he couldn't fault him for being cautious of new arrivals after spending so long operating on his own…

"What, and get locked up as a rogue element?" the Phantom countered, leaning further forward to better glare at the other two men. "Be serious, Sumner; I might have saved this city for your expedition on at least _two _occasions since you got here, but as far as you're concerned, I'm just a rogue cannon who shouldn't be anywhere _near _this city, and if you hadn't had the hive-ships to deal with I've have been stuck in a cell and pumped for information the second I showed my face. Right?"

For a moment, the three men could only stare silently at each other, the Phantom's ability to return Sumner and Everett's dual glares disconcerting the colonels almost as much as his mask, only for the temporary stalemate to be broken as the city's alarms began to blare.

"Control room," both colonels said, automatically reaching for their radios (Neither colonel had been comfortable with giving the Phantom a radio; he was under orders to stay with one of them at all times in the event that he felt the need to give orders).

"Sirs," the voice of one of the new marines said over the radios, "we've just detected a wave of darts, inbound."

"On our way," Sumner said simply, before he turned to look pointedly at the Phantom. "Get to the chair; we'll finish this later."

"Naturally," the Phantom said, as he turned to leave the room before glancing back. "So, which of you will be my 'chaperone' this time?"

"I'll do it," Everett said, glancing over at Sumner as he spoke. "You've got better experience with the city; the men would feel better with you in charge."

"Right," Sumner said, nodding at his old friend before his gaze returned to the Phantom. "We'll finish this later."

"I'm sure," the Phantom replied simply, before he turned around and walked out of the room with Everett, heading for the control chair room with a resolute stride.

Once again, Everett wished that he didn't have to work with such an insubordinate _pain_ to get the job done…


	34. The First Waves

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Not entirely certain about this chapter, but things should pick up later; I have more definite plans for future episodes (Particularly relating to my new take on such classics as "Conversion" and "The Long Goodbye")

The Phantom of Atlantis

Even as he sat down in the chair, John wished that he was as confident in his ability to use the chair as he'd claimed to be when talking with the colonels to convince them to work with him.

He'd tested it out now and again in the past when he'd had nothing else to do, of course, but he'd never gotten into the habit of regularly practising with firing the drones or raising the shield like he might have liked; the only thing he'd regularly done from the chair was pilot the jumpers by remote, and that had mostly been for the sake of it to see if he _could _control the jumpers that way.

It wasn't like he hadn't had his reasons for not practising using the chair in greater depth, of course- his drone supply was limited and he couldn't do much with the shield without risking water damage to the city-, but he'd still given the others the impression that he was better-trained with this thing than he actually was; he could only hope that his practical abilities would be enough when the time came. He'd practised enough with other Ancient technology that he was fairly confident he knew what he was doing, but that still didn't mean he felt _entirely _comfortable with his first time genuinely trying to control something this big and powerful being in the middle of a combat scenario…

He didn't even need the subconscious access to the sensors the chair gave him- just enough to know where enemy objects were going to be so that he knew where to strike- to know that the city was even now preparing to fight back against the Wraith darts; all he needed to know right now was a clearer picture of where the darts were so that he could be sure he wouldn't be wasting drones.

On the bright side, the drones themselves were nigh-on indestructible, which at least limited the possibility of them being taken out by friendly fire; the problem for _him _right now was that finding the darts when they were far enough away from the city that he could be sure he wouldn't be taking out something that the conventional guns were about to destroy themselves- there was no point using drones on something that could just as easily be shot down by the rest of the expedition members-, while still being close enough to ensure that he could use the city's sensors to accurately direct the drones towards the darts…

Then the lights went off around him- the chair responding to his decision to conserve energy; he was going to keep the shield deactivated until the time was right and otherwise work on making it hard for the Wraith-, and John allowed his mind to 'sink' into the chair, reaching deep into the city's sensors as he prepared for the upcoming assault.

As the darts reached the outskirts of the city's sensors, John sent a few quick drones up into the air to eliminate the first wave of darts as soon as possible, only for the next wave to get past the city's outer limits and within range of the gun batteries before he could bring the city's sensors to focus on them. For a few moments, all his attention was focused on the darts as they ducked and weaved around the towers, his mind not even registering the presence of Colonel Everett as the new colonel yelled at him to do something…

_Well, OK, maybe I _am _aware that the guy's yelling in my ear all the time_… John reflected, the part of his mind that was still aware of his immediate surroundings rather than the city's sensors registering Everett ordering him to stop lying around and _do _something…

_Fine_, John reflected, his hands clenching the chair as he focused his attention on the sensors. _Firstly, make sure I know where those rail guns are_…

A few seconds' analysis of the sensors was enough to allow him to determine where the guns that Everett had installed were located- he'd been initially more concerned with making sure the pilots knew how to operate the jumpers rather than looking at where the guns had been installed, trusting the colonels to establish a suitable defence perimeter- based on such details as where the darts were being shot down and other such factors, subsequently deploying another dozen or so drones to target the darts that were heading for the more vulnerable areas.

Even as the other darts began to fall to the expedition's own weapons, the drones targeted the darts that had evaded the main assault and quickly took them down, destroying the darts' propulsion systems and sending them hurtling to crash into the sea around the city (A couple of darts had begun to attempt kamikaze runs, but he managed to aim the drones at the front of the darts just in time to knock them off-course and send them either into the sea or at the very least divert them to the less vital parts of the city).

After another few moments of waiting and monitoring the city sensors, the man known as the Phantom allowed himself a slight smile.

There was no sign of any further darts approaching the city.

The first wave of the Wraith assault had been defeated.

They'd _won_…

Then he registered reports that one of the gun batteries had gone silent despite sensors showing that area to still be intact, and he couldn't help but curse.

So much for that hope; they _had _taken casualties in the first wave…

* * *

"Why didn't you raise the shield?" Everett asked, looking pointedly at the Phantom as the city's five leaders- Doctors Weir and McKay, the two colonels, and the Phantom- sat around the conference room table, the Phantom currently attracting the glares of his Earth 'counterparts' as he sat at one end of the table.

"Well, in case you hadn't noticed, we _are _rather low on power-" the Phantom began.

"What are you talking about; our ZedPM has _more _than enough power to _raise _the shield-!" McKay began incredulously.

"And, given that we have two hive-ships on their way, no idea how much firepower they possess- I've never exactly been in a position to see what those things can do if they _really _'let rip', you know- and even _less _idea how long we have to wait until we receive any kind of word from _Daedalus_, it seemed more sensible to save that power until we have no other choice _but _to use it," the Phantom countered, leaning forward slightly as he glared pointedly at the Canadian scientist. "We've sustained losses, yes, but it's nothing we can't recover from; on the other hand, if we start using the shield energy indiscriminately with just over ten percent of our full power capacity available to us, we run the risk of being defenceless when the main assault arrives."

Once again, Everett wished that he could accuse the Phantom of being irresponsibly reckless, only to be forced to remind himself that he would have done almost the exact same thing in the other man's position; sometimes you had to let some die to save the majority…

In the end, though, the part that really struck him about the Phantom at this point was the expression in the other man's eyes; a look of loathing and hatred that he barely seemed to be keeping under control.

It wasn't for the Wraith, Everett was fairly certain- he didn't display any signs in his voice when talking about them to suggest he felt _that _strongly about them, even though it was clear he was dedicated to defeating them-, and apart from the initial complications of his arrival the members of the expedition had generally been fairly civil towards him after his presence had been made official, but that still left him no further along towards answering the question of who the Phantom hated so passionately…

Everett shook it off; trying to get inside the head of the kind of man who'd wear a mask on a full-time basis wasn't something he had the time or inclination to deal with at this moment in time.

"Getting back to the issue of those hive-ships," he said, drawing his focus back to the main issue facing them at this time as he looked over at the Phantom, "you're certain you can send the gateships by remote up to those hive ships?"

The Phantom shrugged. "Should be straightforward enough; all I need to do is manoeuvre the ships to avoid the darts and then send them straight into the hanger of the hive-ship when they're not expecting it-"

"Uh… are you _sure _they won't expect it?" McKay asked, looking uncertainly at the Phantom as though reluctant to question someone with the other man's attitude but feeling obligated to make the point. "I mean, if you've been practising doing this kind of thing…"

"I only practised it in the vicinity of Atlantis; the chair's 'range' to control something under these conditions is relatively limited," the Phantom explained, looking briefly over at McKay. "Even if I kept the Stargate open while attempting this strategy, the ships would have eventually shut down or the drones exploded when they went too far from the Stargate for the control chair 'signal' to reach them; the connection between the chair and the gateship drones is… fragile over long distances, to say the least."

"But you _are _certain you can maintain control over the distance required under the present circumstances, right?" Sumner put in, his eyes narrowed as he looked pointedly at the man before him, bringing the conversation back to the matter he was interested in.

"Oh, _that's _not a problem; once the hive-ships get into position, I'll just need a minute or so to work out the quickest route possible to get the fine details worked out-" the Phantom began.

"I'm sorry; go back to the part where the hive-ships need to be in _position _before you'll be able to pull this off?" McKay cut in, looking in more-than-slight fear at the Phantom. "Couldn't you send them out _now_-?"

"The gateships were never _meant _to be flown that way, Doctor McKay; it's stretching things to their limits to expect me just to maintain control of them after sending them to the upper atmosphere," the Phantom interjected, his eyes demonstrating a more-than-slight frustration at the other man's fear. "They _have _to be in position there or it won't _work_-"

Further explanation on his part was cut off as Teyla ran into the conference room, anxiety clear on her face as she looked at Elizabeth.

"Doctor Weir," she said, looking urgently at the expedition leader, "we have an urgent problem; the Wraith have managed to gain access to Atlantis."

"What?" Everett said, standing up to look at the Athosian woman in shock. "How-"

"The _darts_…" the Phantom cut in, realisation and frustration apparently warring for supremacy on what they could see of his face. "I stopped the darts themselves from hitting the city, but a few Wraith must have managed to beam out before I was able to do any serious damage to their systems; if they've managed to gain access to Atlantis to _any _degree…"

The man in the mask didn't need to finish the sentence; everyone listening to him clearly understood what this latest implication meant for their future attempts to defend this city.

"We need to prepare search teams to find them before they can do any damage," Sumner said, getting to his feet and glancing over at Ford. "Get everyone organised; we need to find them as soon as possible-"

"And position guards around the ZPM room and the naquadah generators; we can't afford to take the chance that the Wraith will figure out what's powering what," the Phantom cut in (Sumner briefly wondered how much the man knew about which parts of the city were powered solely by the ZPM and which parts were maintained by their backup naquadah generators, but decided he almost didn't want to know the answer; the fact that he'd known enough to remove a generator that wouldn't disrupt the city's daily operations during that nanite thing was more than enough for him). "Any chance I could be on one of those teams?"

"Excuse me?" Everett said, his initial shock shaken aside as he turned to look at the Phantom. "In case you'd forgotten, you're needed here for when those hive-ships-"

"The hive-ships aren't going to be here for a while, Colonel Everett; even _with _the sensors screwed up like they are at present, it's not going to be difficult for you to get enough of an advance warning of their presence for me to get here in time," the Phantom pointed out, even as he pulled out his weapon and examined his power cell before putting it back in its holster. "From what I detected from the sensors, I'd say that around twenty darts managed to make it into a position to beam something into the city; the city's sensors themselves can't distinguish between Wraith and human life signs- the Ancients never really considered the possibility that anything that wasn't one of them would get into the city without their permission so they never programmed the sensors to compensate-, so we're going to need to rely on those 'Life Signs Detectors' to specifically identify the Wraith during our search."

Everett couldn't believe it; bad enough that this… this _vigilante _had taken over defence of the entire city, but did he have to be so goddamn _good _at it? He'd only agreed to having the guy around in the first place to use his information until the point came when he didn't need it, and now it seemed like he barely managed to get by for ten minutes without this masked bastard taking over…

"_Fine_," he muttered, standing up and looking over at Sumner. "Let's get going; we've got Wraith to track down…"

"You shall not be alone," Teyla put in, stepping forward slightly to draw attention back to her. "My people and I are willing to aid in the search in any way we can."

For a moment Everett thought about turning them down- he already had _one _amateur to worry about; the last thing he needed was _more _of them to worry about-, but quickly pushed that thought aside; if these people had managed to survive in a Wraith-dominated galaxy all these years- coupled with what the files had mentioned about some of them being able to 'sense' the Wraith-, they must have _some _skills that could be useful in this situation.

"Very well," he said, nodding in brief resignation at this latest turn of events. "We'll get you some weapons; we'd better get moving as soon as possible."

"Uh… we'll just… get to work on those time devices for the bombs, shall we?" McKay asked, looking uncertainly at the group around them.

"Good call," the Phantom said, nodding in confirmation at McKay. "Get the timers installed but don't program them with a specific time-frame just yet; I still need to work out a time estimate before you start anything decisive."

"Uh… sure," McKay said, as the military members of the expedition stood up and walked out of the conference room, leaving him alone with Elizabeth as they silently exchanged glances.

Finally, after a few moments of uncertainty, Elizabeth broke the silence.

"Well," she said, shrugging slightly as she looked over at McKay, "you can't say the Phantom doesn't have some interesting ideas, can you?"

* * *

As he stood in the corridor leading to an uninhabited area of the city that the sensors had identified as the location of unexplained life signs, John couldn't help but smile slightly under his mask.

He knew that it wasn't exactly healthy, but he couldn't help it; after so long having to hide from the people he'd long ago sworn to protect in the city that was regarded as his home by practically everyone who knew of his 'legend', it was really rather refreshing to be able to get back to where he'd started, going after the Wraith as they sought their prey.

Admittedly, he wasn't used to dealing with them in _these _conditions- the Wraith had never managed to make it into _Atlantis_ before; that iris was really a _brilliant _means of defence; even without the sea above the city preventing the Wraith finding anything if any of them had managed to track down the planet he was dialling from, they couldn't even come through the gate if he didn't want them there-, but that didn't mean he couldn't adapt.

Hell, if anything, hunting the Wraith here was _easier _than his previous hunts; here he was on territory he knew like the back of his hand (Probably better, now he thought about it; that phrase had never made _any _sense to him), while the Wraith were completely unfamiliar with the layout of Atlantis.

_Plus, of course_, he reflected, glancing ahead of himself to where Lieutenant Ford was walking ahead of him, his weapon drawn as he looked around himself with an anxiety that was only visible to John after such a long experience with human hunters, _the back-up helps_.

He wasn't going to say that it was actually easy for him to start working with other people after so long doing his own thing, but it was rather nice not to have to worry about watching his back…

As a Wraith warrior- one of the big guys with those stupid masks; John had _never _understood how those suckers saw anything in that headgear- out of the shadows to throw the young lieutenant down a nearby corridor, John didn't hesitate; raising his own gun, he stepped out behind the Wraith as it advanced on its latest would-be meal, fired a couple of quick kill-shots at the Wraith- no sense doing things halfway, after all- before walking over to crouch down to check on the lieutenant.

"How are you?" he asked casually, as Ford turned to glare at him while wincing slightly at the pain in his skull.

"Not bad," the younger man said briefly, narrowing his eyes as he looked pointedly at the masked man before him while indicating his gun. "How about next time _I _be the one to shoot the Wraith?"

"Wouldn't work; if I was bait, these guys would just kill me," John said, shrugging nonchalantly as he slid his gun back into its holster. "You're just another human to them, and that means they'll take their time to make it interesting; with me?"

He smiled slightly. "They know the only way they're ever going to feed on me is if they take me out straight away; taking their time with me would only get them killed."

Ford didn't look like he entirely believed the Phantom's explanation, but that wasn't important right now; all that mattered to him was that they were working together to deal with the Wraith.

"_Attention all teams_," Sumner's voice suddenly said over the radio, the colonel sounding slightly breathless. "_Three Wraith just attempted to attack generator number two; whichever team is closest to generator three, report there as soon as possible to provide further assistance_."

Quickly thinking back on the briefing where team layout had been allocated, John remembered that Teyla's team- a predominately Athosian one with just one marine- was the closest team to that area; at least that meant they'd have a clear idea what the Wraith they'd be facing would be capable of, rather than a traditional Earth-originated team.

"_We are on our way_," Teyla said, her voice cutting through his radio, the sound of running in the background as her team moved into position.

Going over the 'grid' he'd created of Atlantis in his head, John smiled slightly as he turned around to hurry towards the area that was most likely to be the location of any as-yet undiscovered Wraith, barely registering the sound of Lieutenant Ford behind him (The Wraith were traditionally heavier than humans so he was fairly confident he'd be able to hear it if any of them attempted to sneak up behind him and Ford without even needing to look).

If any remaining were in that area, he'd prefer to take care of them as soon as possible…

Even as he ran, however, a part of him couldn't help but feel somewhat concerned about the ease with which he'd slipped back into 'combat mode'; even after all the time he'd spent hiding on Atlantis, it still barely took him a matter of minutes to shift back into combat mentality.

For all his attempts to convince himself he was more than a guy who killed Wraith, he kept on slipping back into that roll _far _too easily for his own comfort…

Then another Wraith began to charge down another corridor towards him, and he forced his mind back on topic as he fired his gun at the creature's face; he could worry about what his eagerness for combat said about his psychological state when this Wraith invasion had been dealt with.

* * *

An hour or so later, the senior staff found themselves back in the conference room, the colonels going over the aftermath of the recent 'invasion'- they'd managed to get by with only a few casualties in the teams, mainly since the Phantom's advice about establishing themselves around the generators meant that they'd managed to catch some of the Wraith off-guard and thus limit the available opportunities for the Wraith to take people by surprise- while McKay reported on the progress with the bombs.

"Getting the bombs set isn't the problem; the _problem _is in disabling their original motion-detection settings and reprogramming them to accommodate a timer," the Canadian explained as he glanced around at the others. "We think we've managed to calibrate everything to work correctly with the new systems, but these _are _fairly complicated devices; it's going to take time to make sure we've got everything wired up correctly…"

"In case you didn't notice, Doctor McKay," Colonel Everett said, looking pointedly at the man before him, "those hive-ships are only a day or so away from us in a _best-case scenario_; we need to be _certain _those timers are going to be ready by then-"

"Look, these are nuclear bombs we're dealing with here; we need to be _careful _if we're going to avoid blowing anything up-" McKay countered.

"Look, just do what you can and then get everything together; this is _not _the time to start arguing about this stuff, OK?" the Phantom said, standing up to glare pointedly at the two men before turning to look at Elizabeth. "If you don't mind, I think I should get to the chair room right now and get a little practise with that remote control thing; let me know when the hive-ships are within range."

"Already on it; we have a gateship keeping an eye on things ready to let us know when the ships come within range of the planet," Sumner put in, looking at the Phantom in a very pointed manner, evidently almost insulted that the Phantom had addressed a military-based announcement to Elizabeth rather than to him or Everett.

"Ah, good," the Phantom said, moving past the initial discomfort like it didn't exist as he looked at the other man. "He _does _know he's to time approximately how long it takes him to get from the ship to Atlantis once they take up orbital positions, right?"

"_Yes_," Everett said, his teeth gritted slightly as he looked at the Phantom, once again insulted at the other man's casual assumption of command even as he was unable to contradict any of the orders the man was giving. "He's even going to go at regular speed to ensure the… _conditions_… are accurate."

"Good," the Phantom said, nodding once more before he glanced over at McKay. "Let me know when those timers are ready; once I know how long it takes to get to the hive-ships from here I'll let you know what time I need."

"Uh… check," McKay said, his comment apparently only being registered by the Phantom's back as the man stood up, turned around and left the conference room, his black cloak trailing behind him as he walked through the door.

After a moment's silence, McKay spoke again.

"Blunt kinda guy, isn't he?" he said, indicating the door where the Phantom had just left.

"He knows when to cut through the crap and get to the point," Sumner said, his tone admitting a brief, if grudging, respect for the man. "Have to respect that, when you get down to it."

"Whatever you think of his methods, he makes a valid point; if we don't keep on working, we're going to have a problem when the Wraith get here," Elizabeth said, looking around the table before her gaze focused on Sumner. "Colonel, I assume your men are still ready and able to man the defence?"

"What they can work, they will," Sumner said, nodding in confirmation at her.

"Then we need to make sure everyone who can fight is ready to do so; we've dealt with everything from the first wave, but that still leaves the second wave on their way and no sign yet of the _Daedalus_," Elizabeth said, looking pointedly at everyone around her to make sure they understood what she was saying. "Prepare to evacuate the injured to the alpha site- we can't afford to waste the energy needed to dial Earth at a time like this-, and then get everyone else into position immediately; we _have _to hold this city."

* * *

As John sat back in the Ancient control chair, his mind keeping a close 'eye'- for lack of a better term; keeping a close 'thought' always sounded slightly stupid to him- on the sensors for any sign of the Wraith hive-ships, Doctor McKay monitoring the chair's systems- he insisted on making sure everything was working right in this situation personally no matter how many times his team assured him everything was fine-, he allowed himself a brief smile as he heard Elizabeth's voice begin to address the city; something about her continued presence there made him feel… better, somehow (He knew why that was, but wasn't too keen to analyse it in great depth; things were complicated enough without _that _getting involved right now).

"_This is Weir_," she said, her voice clear as she spoke to her people. "_Now I know how tired you all are, and how much we have asked of you these past few days. Hopefully the _Daedalus_ will arrive soon, but until that happens our fate is in our own hands. If during the course of this battle our mission fails, I will give the order to evacuate to Earth; we all hope that won't be necessary, but we are not to hesitate if it does. That is all_."

John barely had the time to smile in approval at her statement- effectively covering everything they needed to know about the current situation while also encouraging them to hold on and not give up-, before a less welcome voice spoke to him directly.

"_Sumner to Phantom_?" a voice said over the radio, breaking him out of his brief reflections and bringing his attention back to the matter at hand.

"Yeah?" he said, reaching up to tap the radio they'd given him (He'd deactivated the one he'd installed in his mask; as long as he was working with the rest of the expedition, he didn't think it would be the best idea to let them know just how much he knew about them).

"_Gateship Four just contacted me_," Sumner explained. "_They said that, allowing for the assumption of a gradual speed to adjust for potential dart impact, it should be possible to reach a hive-ship in around four minutes_."

"Right, got that; tell the pilot thanks for his assistance," John said, quickly shifting the radio link- Sumner would understand; with the city itself at stake he didn't have time for a polite goodbye- to address the scientist currently overseeing the placement of the bombs. "Doctor Zelenka, program the timers on the bombs for four minutes forty seconds, to begin when I give the signal; that should be enough time to reach the hive-ships' main hangers."

"_Affirmative_," the Czech scientist replied briefly before returning to his original task, leaving John to sit patiently for another few moments, his mind briefly drifting to thoughts of Elizabeth- she'd really been _brilliant _in that conference room; quietly but firmly exerting her authority over the colonels almost without them realising it- until…

"_They're sending in another wave_!" Elizabeth's voice yelled over the radio, spurring the part of John's mind that would always think like a soldier back into action.

Shifting his focus back to the short-range sensors, John noted that she was right; darts were already approaching the city, in far larger numbers than the first time around.

Fortunately, _this _time around they were closer together…

John didn't hesitate; with their drone supply depleted, his original strategy wouldn't work, so it was time to go back to something he'd wanted to do the first time around. As soon as the darts were close enough, he activated the shield, sending the darts crashing into it before they could pull away, only dropping the shield when the last few darts in the wave pulled up to avoid striking the shield like their predecessors had; from what he could tell, there were enough darts left for the city's Earth-originated defences to pick them off in relative comfort.

He jut hoped that there weren't enough darts left to beam a few decent-sied Wraith strike teams into the city before they were all destroyed; they did _not _need another round of hand-to-hand with _those _assholes…

"Wow…" McKay muttered- admittedly in a low voice; clearly he didn't want to admit to being impressed by something someone else had done- before he turned to look at the man in the chair as another thought occurred to him. "Hold on, what happened to 'not wanting to waste power'?"

"Well," John said, shrugging slightly as he looked at the Canadian standing beside him, "I figure that, given how long we've got until the _Daedalus _is meant to arrive, we can afford to waste a little energy at this juncture."

"And if the _Daedalus_ _doesn't _arrive?" McKay asked, glaring critically at the other man.

John shrugged. "If it doesn't arrive in time, we're probably going to be dead; what good will power be to us then?"

After a brief silence, McKay sighed.

"Y'know, do you ever wish you _weren't _right all the time?" he asked.

"That depends; how do _you _feel when you realise that you were wrong about something?" John asked, raising an eyebrow at McKay before he leant back in the chair. "On second thoughts, don't answer that; I _really _need to concentrate at this point…"

Reaching out with his mind for the jumper that they'd loaded the first bomb into, John activated the gateship's drones at their lowest level- just enough to get them moving without being so powerful that they'd risk blowing something up-, and, after receiving confirmation from Zelenka that the time had been activated and he was clear of the ship, sent the gateship up through the tower, his mind fixed on monitoring the sensors to avoid incoming darts even as he pushed the ship onwards and upwards as quickly as he dared.

_Here we go_… he reflected, allowing himself a slight smile as he drew in ever closer to his target. _Scratch one more hive-ship_…

_Right_…

_About_…


	35. The Coming of the Daedalus

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

_Now_.

As John sat in the control chair, for the first time in his life he regretted one key feature of this city; they didn't have any cool viewscreens to allow him to really _see _what was happening out there. The sensors provided a pretty clear picture of what was going on, of course- the sight of the hive-ship blowing up like that was almost worth the loss of a decent jump- _gateship_; if he started slipping up and naming them what _he _wanted to call them he'd attract more attention than he really wanted- to deliver the bomb.

_One down_, he reflected, allowing himself a slight smile as he turned his mind back to the issue of waiting for the next bomb to be loaded onto the next gateship for deployment, _one to go_…

"_Attention Atlantis_," an unfamiliar voice suddenly said over the city-wide broadcast system. "_This is __Colonel Steven Caldwell, commander of the _Daedalus_; we are ready to assist you_."

John blinked.

_Daedalus _was here already?

He wasn't sure whether to be impressed or frustrated at their timing; on the one hand, they _had _managed to arrive before the hive-ships started anything too drastic- the damn things hadn't even activated any of their weapon systems yet-, but on the other hand there _was _the issue that they hadn't managed to get here soon enough to provide them with an alternative means of taking out the damn hive-ship…

"_Weir to Phantom_?" a voice said, this one over his 'public' radio (The one the expedition knew he possessed).

"Yes?" he asked, raising his hand to activate the radio in response.

"Daedalus _has beamed down the ZPM and McKay is taking it to the power room as we speak_," Elizabeth's voice said, prompting a brief smile from John; at least _that _side of things was going according to plan. "_However, he's uncertain how the system would respond to another ZPM being inserted if the city's power is already being used for some purpose; he wants me to confirm with you that you won't raise the shield until he's installed the new ZPM and all power can be directly diverted to the shield_."

"Understood," John replied, nodding briefly as he reflected on McKay's request. The scenario he'd proposed was a bit of a question-mark, of course, but if he couldn't be certain what would happen if the ZPM was connected under the conditions McKay was concerned about, he couldn't risk activating the shield until McKay had accomplished his goal; if you could get electric shocks from pulling out a plug while the power was on, he _really _didn't want to know what could happen if you made a similar screw-up with zero point energy power sources.

As he sat anxiously in the chair, the sensors monitoring the battle waging above them- the hive-ship's sheer size and dart cover weren't exactly making it easy for the _Daedalus_, but the _Daedalus_'s shields and its smaller structure made it harder for the hive-ship to do any damage in return-, John was already preparing himself for the moment when he might have to send up another gateship to take out the other hive-ship if the current fight didn't go their way…

Once again, he found himself missing the thrill of battle; he might be more useful to the expedition in the control chair than he'd be out there trying to wage a one-man war against the Wraith groups still in Atlantis-, but at least out there he _knew _that he'd be making a difference; right now all he was doing was waiting for his cue. With the _Daedalus_ up there firing away at the hive-ship, there were too many darts in motion for him to even _attempt _to send the next gateship up in case it collided with a dart before it reached the hanger, and he wasn't going to try and waste the gateship's drones in an attempt to attack the hive-ship when there were this many darts around; in the end, all he could accomplish at the moment was to sit around and wait for an opportunity to serve as essentially a human 'on/off' switch.

_God_… he groaned, leaning back against the chair and closing his eyes in reflection. _This is just _great_; even when I'm actually _doing _something I wish I was back out there kicking Wraith ass_…

He might have needed to learn how to fight Wraith to survive, but did he have to have reached the point where he enjoyed it _this _much? Elizabeth was a _diplomat _by nature; she'd _never_-

NOT_ gonna go there_! John berated himself, stopping that line of thought instantly; he'd already promised himself he wouldn't go there, why couldn't he _stick _to that…?

The sudden awareness of a massive explosion on the sensors drew John's attention back to the battle waging above him, prompting a brief smile as he 'saw'- as much as he could be said to 'see' anything when the information was being transmitted directly to his brain by the chair- the second hive-ship blow up at last, followed closely by the remaining Wraith cruisers; evidently the cruisers had decided that now was the time for a tactical retreat rather than remain to fight something that had already taken out three of their main ships.

Then he noticed the remaining darts turn around and begin to head towards Atlantis, and instantly re-evaluated his original assessment of the situation; at the rate those things were going, by the time they hit Atlantis they'd be the equivalent of seriously massive bullets moving at a rate that could easily shatter _any _part of the city they hit…

It was official; they were in trouble now. With that kind of destructive force arrayed against them, if McKay didn't get that ZPM installed soon-

"_OK, Phantom_," McKay's voice said, cutting off his train of thought- a fact that he was particularly grateful for as it wasn't going anywhere pleasant-, "_I've got the ZedPM plugged in; get that shield _on!"

John was just about to do what McKay had ordered him to when he checked the city's power supply and noticed a problem.

"Doctor McKay?" he said, trying to keep the frustration in his voice to a minimum as he . "As much as I admire your enthusiasm for your job, you _do _know that you need to actually _insert _the ZPM to the power systems rather than just put it in the hole, right?"

For a moment McKay was silent, evidently processing what he'd just heard, before he spoke again.

"_What; and you couldn't have mentioned that _before _now_?" he yelled, the Canadian scientist sounding increasingly panicked even as John's sensors told him that the city was powering up once more. "_I thought it descended into the power core as energy was used up_-"

"_Later_," John said, cutting McKay off as he activated the shield, drawing on a power supply far greater than what he'd been accessing so far, allowing himself a brief smile as the darts- their speed too great for them to stop themselves like they had done when he'd erected the shield earlier- crashed into the shield, generating small explosions (They might have been powerful enough to damage Atlantis but with two ZPMs to draw power from the shield was capable of coping with far more destructive forces than _that_) against the shield.

For a few seconds John just lay back in the control chair, smiling in satisfaction at the 'feel' of Wraith darts colliding with the city shield while otherwise doing no damage, until he shook that thought off, turned the shield over to the main control room- leaving it activated, of course; with Ancient technology you _really _had to be careful what you thought-, got out of the chair and headed for the door.

He'd done all he could do here for the moment; right now he'd probably accomplish more back in the main control area.

* * *

Looking up at the sound of footsteps, Elizabeth allowed herself a brief smile at the sight of Jo- _the Phantom_ entering the main control tower, a casual smile on his face as he walked over to the control room to join her and Colonel Sumner; Everett was still out looking for any Wraith that might have remained in the city after the initial assault.

"OK, shield control has been rerouted to respond to orders from here; what's the situation inside Atlantis itself?" the masked man asked, looking casually around at the city's two main leaders.

"We've lost contact with Colonel Everett's team somewhere in the southern area of Atlantis, and Lieutenant Ford's team has been discovered with the lieutenant himself missing," Sumner explained, his expression grim as he looked at the man he was only grudgingly working with even now. "According to all available information, we still have maybe around a dozen Wraith unaccounted for in the city- it would have been more if it wasn't for that stunt you pulled with the shield during the first wave-, but we still have to find them on the city's sensors; any assistance you can provide would be welcome."

"Hunting Wraith?" the Phantom said, smiling slightly under his mask as he pulled out his weapon, checking its power cell before he glanced back at Elizabeth. "So long as you don't need me for anything else somewhere else, I'm there."

"Well…" Elizabeth said, briefly contemplating making up a task that would allow her to spend time with him- how often would she get this kind of opportunity to ask John about where he'd come from without worrying about being discovered?-, before she decided against it; as he'd so accurately pointed out on previous occasions, he was their best available expert at fighting the Wraith in any area. "No, you can go."

"Right," the Phantom said, nodding briefly at Elizabeth before he turned to look at Sumner. "If you're having trouble finding Ford, try widening the sensor radius; it's possible he fell somewhere outside the city itself."

With that, the Phantom turned around and walked over to join the rest of the marines as they began to gather their weapons in preparation for the search, leaving Sumner and Elizabeth to look reflectively after him before Sumner broke the silence.

"Interesting man," he said simply.

"Excuse me?" Elizabeth asked, looking at Sumner with barely-restrained surprise; had the colonel just said something _positive _about the _Phantom_?

"I'll give him this; he knows what he's doing when he gets into a fight situation, and he knows how to operate Ancient technology with a skill that makes the best men we've got seem like nothing but rank amateurs," Sumner said, his tone slightly grudging even as he spoke- evidently he wasn't entirely comfortable giving a man who was officially a civilian this kind of praise-, his gaze fixed on the Phantom as he left the control room with one of the teams. "What I _don't _get is where he _learned _all this…"

Elizabeth was about to ask if that mattered before she stopped herself, realising that it actually tied in to what she herself had been wondering about John; where _had _he learned how to do everything he was capable of? Had he picked up his fighting style on his home planet- wherever that was-, had he learned how to fight after coming to Atlantis, how had he found out about the city and gained access to it in the first place…?

As much as Elizabeth felt that she could trust John, she couldn't shake the fact that she really knew remarkably little about him…

"Colonel Sumner?" the distinctive voice of Doctor Zelenka said from off to the side, prompting the colonel and Elizabeth to look at where the Czech scientist was currently standing beside a screen displaying the layout of Atlantis. "We believe we have found Lieutenant Ford…"

"You have?" Sumner said, looking curiously at the Czech scientist. "Where is he?"

"That's part of the problem," Zelenka said, indicating an area on the map just outside of Atlantis, a small white dot blinking in a position that had to be at least a couple of hundred metres away from the rest of Atlantis (Elizabeth had never bothered to calculate the specific size of the city herself, but she knew that it had to be fairly large). "He's out here."

Elizabeth didn't need to be a medical doctor to know that it was a miracle Ford was still able to give off any kind of signature for the sensors to detect; even without the recent battle they'd been dealing with and the odds of him getting caught in the crossfire,

"Colonel Caldwell?" she said, activating the radio link to the _Daedalus_; questions of how Ford was still in a condition to give _any _kind of signal could wait until he'd been recovered. "One of our men is in the ocean outside our shield, most probably injured. Can you beam him to your ship and then down to our infirmary?"

For a couple of moments there was only silence, the disappearance of Ford's signal from outside Atlantis the only sign that the _Daedalus_ was doing what they had asked- the signal had vanished too rapidly for the reason it had ceased to be Ford's death-, until Carson's voice broke the silence.

"_Colonel Sumner; Doctor Weir_?" he said, evidently anxious about something. "_You'd better get down here immediately; we have a bit of a… problem… involving Lieutenant Ford that I think you should know about_."

* * *

A couple of hours later, as John stood in the infirmary, the last few Wraith in the city having been eliminated by the search teams- there was no time to worry about attempting to interrogate prisoners when they could have another wave of hive-ships on them at any moment; they just didn't have the resources available to have people guarding the Wraith while they needed every man possible available to man the city's defences-, he couldn't help but wonder if there was something he could have done differently that wouldn't have resulted in the current situation.

Glancing over at where Everett lay in a nearby bed, the man having now aged at least a dozen years since his arrival in Atlantis, John almost couldn't decide who was better off; Everett seemed pretty shaky, but there was at least every chance he'd recover enough on his own to live some kind of normal life, even if he'd need to relocate in order to preserve the secret of the Stargate Program.

Ford, on the other hand…

Even as he looked at the young man lying before him- Sumner and Elizabeth had already moved on to get status updates on the rest of the wounded in the infirmary-, John couldn't help but recall his own experiences with Wraith enzyme.

Ever since he'd killed a Wraith just as it was starting to feed on him- he sometimes wondered how much it had taken from him before he could reach his gun, even after later tests confirmed it could only have been a couple of weeks' worth of life at most- and felt that rush of strength and mental disorientation caused by the enzyme overdose for the first time, the power he'd felt with the initial a sharp contrast to his status after he crashed and burned when the enzyme burnt out of his system…

Even after almost a decade since that close call, the memory of how close he'd come to becoming a Wraith junkie- for lack of a better term- continued to haunt his nightmares on more than one occasion.

He was just lucky that he'd made it back to Atlantis while the enzyme was still strong enough in his system to analyse it on the city's medical scanners; once he'd determined the effect it had on him, he'd resolved to himself never to use _that _stuff again unless all other options were exhausted.

He might try to maintain some ethical standards, but when you were on your own and facing a galaxy full of Wraith, you had to sometimes put ethics aside in favour of practicality. He tried to save it for when he had absolutely exhausted all other options available to him, but more than once he'd reached a point where he'd no other choice but to use the enzyme to increase his chances; he just always made sure to limit it to no more than what was absolutely required to survive the current crisis.

And now here was Ford- the lieutenant was really a decent enough kid, even if he was a bit rigid in obeying orders at times-, doped up to the eyeballs with the stuff and literally _dependent _on it for his body to function.

John couldn't help but shudder slightly at the thought of what he might have done to himself if he hadn't retained enough coherent thought to scan himself while the enzyme first entered his system.

He'd thought that he was a monster as he was; with something like the Wraith enzyme in him permanently…

"_Weir to Phantom_," Elizabeth's voice suddenly said over his radio, cutting off John's train of thought (A fact that was probably for the best, John admitted; that kind of thought _never _got him anywhere).

"Yes?" he asked, tapping his ear to activate the radio.

"_Doctor McKay just activated the city's long-range sensors_," Elizabeth said, her tone alone making it clear that she was concerned about whatever she had to tell him.

"Let me guess… more hive-ships?" John asked, taking care to keep his voice low as he glanced around the infirmary; if they weren't publicly announcing anything yet, he wasn't going to be responsible for starting a panic.

"_Twelve, to be precise_," Elizabeth confirmed. "_We're planning on sending _Daedalus _out to try and stop them before they can reach us- given that our shield only buys us time and our ability to defend Atlantis is limited, Sumner and Caldwell have concluded that our best chance is to take the fight to the Wraith-, but given that you mentioned previous experience_-"

"Sumner and Caldwell want to know if I'll be willing to give them a few pointers about how to take them out, huh?" John said, allowing himself a moment's silent contemplation before he nodded resolutely and turned to walk out the door. "OK, I'll do it; just so long as they're not expecting me to go with them on _Daedalus_, all should be fine."

"_Understood_," Elizabeth said, terminating the call as John began to head towards the conference room.

He might be fighting with them to defend Atlantis from the Wraith, but John didn't kid himself into thinking that this meant that they'd accepted him; after Sumner had spent the better part of the past year hunting him, he'd be an idiot to willingly enter a confined area like the _Daedalus _for any reason.

Atlantis might be equally confined in its way, but he knew the territory here and could plan an escape from pretty much anywhere they tried to stick him; if Sumner reverted to his original plan to try and capture him and _make _him talk, it would be far easier to pull it off in the confined and unfamiliar _Daedalus_ than in the city which the Phantom had lived in for the last twenty years.

The trick now, as far as John was concerned, was working out the best way to give everyone the information and assistance they'd need to survive without giving away the fact that Elizabeth was still the only person on the senior staff he felt certain he could trust…


	36. Be More Like Me and Be Less Like You

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

The Phantom of Atlantis

A few hours later, as John sat in the control room of Atlantis- the room which had for so long been his private domain, before the expedition arrived and forced him into hiding-, he couldn't help but feel the slightest twinge of inappropriate hope at the fact that Elizabeth trusted him enough to give the order that allowed him to take up position here in the first place (He might not be _explicitly _in charge, but he was still going over the city's defences and coordinating the troops in Sumner's absence; a definite step-up from where he'd been mere days ago, to say the least).

He knew that her decision was based more on practicality than anything more- with Sumner having accompanied Caldwell on the _Daedalus_ and Everett being shipped back to Earth with the rest of the wounded he was technically the superior military expert in terms of organising the city's defences; even Everett's forces had deferred to his superior knowledge of their enemy and available resources-, but a part of him still couldn't help but feel that there was more to her reasons than that; she hadn't even bothered to assign anyone to keep an eye on him to make sure he didn't do anything he was supposed to…

He shook that thought off; Elizabeth was just basing her actions on the fact that they'd spent time together before and he'd always stuck to his side of their various deals and discussions, there was _no_… deeper meaning… behind it.

God, _I'm thinking too much about this_… he reflected to himself, trying to force that pointless train of thought to stop before it got much further; wishing for the impossible was _not _going to help anything right now.

In terms of practical wishes, he just wished that the Wraith would reach the location where McKay had calculated they'd have to make their last 'stop' before reaching Atlantis sooner rather than later; at least once they were there they'd know whether their plan for taking out the rest of the hive-ships was going to work or not.

The thing that frustrated him most about the current crisis were those moments when he couldn't actually _do _anything to actively contribute to the city's defence; when he wasn't making an active difference, he felt like he was just waiting for the other shoe to drop and somebody to march in and try to arrest him…

The sound of everyone else in the control room falling silent- accompanied by the sound of rapidly-approaching footsteps- prompted John to glance up from the laptop that he was currently studying- he'd been checking the positions of the railguns in case anything needed to be relocated after the damage caused by the Wraith earlier-, to see an unexpected new arrival in the control room.

"What the… Lieutenant _Ford_?" he said, turning to look at the new arrival even as the other man stared back at him, his left eye now completely black and the skin around the eye distorted as though it had been burned by something.

"Reporting for duty, _sir_," Ford said, standing to attention as though nothing was amiss about his appearance, his tone making it clear as he glared at the man before him that he would rather report to anyone but a masked man who'd shot him the last time they'd come face-to-face.

"In_ that _condition?" John countered, folding his arms as he glared at Ford. "Lieutenant, as much as I respect your desire to help, right now you're doped up to the eyeballs on Wraith enzyme; you're in no condition to take part in _anything _to do with protecting-"

"I'm a trained soldier with detailed tactical and explosive knowledge; I _think _I can contribute more than some talented amateur-" Ford began.

"I've been killing Wraith since before you even _entered _the military, _Lieutenant_; I thinkyou should consider _yourself _the amateur in this situation," John countered, his arm folded as he glared at the lieutenant. "Even if we were dealing with something you _had _encountered before, you're in _no _shape to try and coordinate anything; you have to go back to the infirmary-"

"I don't take orders from _you_!" Ford yelled, grabbing John by his cloak and hauling him out of the chair, pinning him to the console before John could stop him.

"Point… taken…" John muttered, even as he slowly moved one hand underneath his cloak towards his gun. "However… I have… other… methods… of making… you stop…"

With that, he pulled out his gun and fired it directly at Ford's chest, the point-blank-range stun blast sending Ford collapsing to the ground in a heap just as Doctor Beckett and a couple of other members of the medical staff hurried into the room, looking anxiously at the lieutenant.

"Is he-?" the Scottish doctor began.

"Just stunned, but he is _definitely _not going to be fit for doing anything any time soon," John replied, slipping his weapon back into its holster as he looked at Beckett pointedly, ignoring the stares from the rest of the people in the room. "You need to keep a better eye on your patients in this condition; the last time I encountered this, the poor bastard went and practically burnt himself out trying to fight three Wraith in hand-to-hand before they all fed on him…"

"_All _of them?" Beckett asked, his eyes wide as he stared at the Phantom.

"Mass enzyme overdose meant that it took a lot more to put him down than it would have done if he was normal," John said, shrugging dismissively as he tried to conceal his own memories of that particular failure; he'd tried to break out of a hive-ship after it got lucky with the aid of a couple of prisoners, but in the end both of them had died when the enzyme he was forced to give them as a 'boost' resulted in them becoming so irrational that they pushed themselves too far and ended up being fed on while he escaped. "As you said, the enzyme makes them stronger so the Wraith can take their time feeding on the victim; they don't do it that often, but overdosed victims can provide a _great _deal of energy when the need arises."

"Right…" Beckett said, nodding slightly uncomfortably as he looked at John- clearly concerned about how John had come by that information-, before he turned to the rest of his team. "Let's get the lieutenant out of here."

"Good luck with the 'weaning', by the way," John said, nodding slightly at the other man as Beckett's staff picked Ford up.

"We'll… do what we can," Beckett said, nodding at the masked man as he began to follow his men out of the control room, leaving John to return his attention to the matter of the city's defences. He was just about to contact a couple of members of the science team- he might be able to divert a bit more power to the city's weapons systems if he could work out a means of transferring drones from the jumpers to the city- when Elizabeth walked into the room, looking anxiously at him.

"Problem?" John asked as he stood back up to look at her.

"We just got word from the _Daedalus_," Elizabeth replied, her expression grim as she looked at John (Communications to the _Daedalus _had been diverted to Elizabeth's office while the staff in the control room focused on coordinating the city's military efforts, thus limiting the potential distraction from their work that might result from the _Daedalus_'s messages). "They managed to destroy two hive-ships, but the other ten have managed to work out a way of negating our teleportation frequencies and are still approaching Atlantis."

_Damnit_… John muttered, cursing himself for allowing himself to feel even _slightly _optimistic at their chances; he should have _known _the Wraith would have a way around teleportation after all the Ancient information he'd found on the topic.

"What's the plan now?" he asked, deciding to cut straight to the chase. "I mean, aside from the obvious one of getting everyone behind the shield to think of something…" He paused as he took in the expression on Elizabeth's face. "That's it, isn't it?"

"We were wondering if you could offer any further suggestions…" Elizabeth began, her slightly hesitant tone prompting John to put a lid on his aggression before he unleashed it; the last thing he wanted was to give _Elizabeth _reason to be uncomfortable around him after everything he'd done to try and assure her that he _could _be trusted.

Even if he could never deserve… to be _that _close to her… he could at least have her friendship; in the end, it was more than he had a right to expect, and he should be content with that.

* * *

After the _Daedalus _had landed at Atlantis's west pier- damage sustained during the confrontationmeant that the ship would have to make full use of Atlantis's shields until it was repaired-, Colonels Caldwell and Sumner swiftly joined the rest of the senior staff in the conference room to go over their next plan of attack. With the Phantom having barely managing to re-establish the shield before the Wraith bombardment started- there hadn't been time for him to return to the chair so he had been forced to activate it from the control room-, the small group were now brainstorming any ideas that might allow them to figure out how to deal with the Wraith assault before the ZPM ran out (Which, according to Doctor McKay, would only be in a matter of days due to their possession of only a single ZPM and the scale of the Wraith bombardment currently facing them).

"We have to face facts here," Sumner said as he looked around grimly at the assemblage of people before him. "Even if we destroy these hive ships right now, more are just going to show up, and we have no way of knowing how many there actually are out there."

"Coupled with the fact that Atlantis is the only way to get to Earth- and, from there, to the rest of the Milky Way galaxy-, I think it's safe to say that they're going to keep coming for as long as we're here," Doctor Weir added, the expression on her face making it clear that she was aware of the implications of her last statement no matter how much she disliked them.

If they couldn't defeat the Wraith, their only option might be to destroy Atlantis…

"As long as they know we're here…" the Phantom muttered, nodding thoughtfully as he leant back slightly in his chair his eyes closed underneath his mask as he thoughtfully clasped his hands and tapped his chin with his index fingers.

"What?" Sumner asked, turning to glare pointedly at the other man; right now he was in no mood for any more of their strange ally's enigmatic bullshit.

As though Sumner's words were a cue, the Phantom's eyes snapped open as he looked sharply over at the lieutenant colonel, a slight smile on his face.

"I have a plan to… well, if it works, we _should _manage to drive the Wraith off without needing any back-up…" he said, the grin slightly fading from his face even as he spoke, as though he'd just realised something he'd overlooked earlier, before continuing, "but… I'm going to need Teyla's help if we're to have any hope of pulling it off."

"My help?" Teyla asked, looking up uncertainly at the Phantom's last comment. "In what way may I be of assistance to you?"

"Well… that's a _bit _of a complicated story…" the Phantom said, looking uncomfortably around at the other people in the room before his gaze settled on Sumner and Caldwell, evidently concluding that they were the people he needed to address more specifically with his latest news. "What I'm about to tell you is going to be… potentially disturbing… but I can assure you that it is _not _as drastic as you might think, and I would appreciate you hearing me out before you make any decisions about how to respond to it."

After a moment's solemn silence, Sumner nodded.

"All right…" he said, trying to conceal just how puzzled he was at the Phantom's request even as he recognised that he wasn't as concerned about it as he might have been earlier.

After the man had so far cooperated fairly effectively with him and Dillon during the initial Wraith assault, Sumner supposed the Phantom had earned _some _leeway in his dealings with them, even if the mask and the lack of information about their mysterious ally's past still made the colonel uncomfortable…

"Thank you, Colonel," the Phantom said, nodding briefly at the colonel before he turned back to look at the rest of the people in the room. "In a nutshell, the reason that Teyla and some of the other Athosians are able to sense the presence of the Wraith is because they have Wraith DNA."

Teyla's eyes widened in shock.

"_What_?" she said, looking at the Phantom as though she wasn't certain whether to be horrified or outraged at what he'd just said (Not that Sumner could blame her; the idea of sharing _any _kind of ancestry with those things would be enough to creep him out, and he hadn't spent his life fearing that he'd be killed by those assholes).

"It was part of a Wraith experiment conducted by one of their scientists after he went rogue a few decades ago," the Phantom explained, looking at Teyla in a conciliatory manner, evidently trying to apologise for revealing this to her so suddenly. "He was trying to… well, 'improve the food supply' by blending human and Wraith DNA- Wraith life energy tends to be more potent than human, but they traditionally avoid feeding on their own kind; it's a whole thing regarding their belief in their superiority over us that makes it more 'acceptable' to hunt us rather than each other-, but he had to abandon the experiment when he found out that the DNA he introduced to the subjects' genetic makeup also gave them access to the Wraith telepathic network; he assumed that subsequent interbreeding with normal humans would dilute the Wraith genes out of the population after he ended the experiments, but things didn't quite work out that way and at least some of the subjects' children retained some degree of awareness of the Wraith psychic network."

"And you know this… how?" Sumner asked, looking critically at the Phantom.

"I found the lab where the scientist conducted the experiments a few years back- damn thing had been abandoned for centuries; the Wraith generally don't bother cleaning up after themselves- and, after checking over the data he'd left behind, I tracked the subjects he'd released back to their relevant home planets to check on what had happened to them," the Phantom said dismissively. "None of them seemed to be harmed by what had happened to them, and baring a slight 'sensitivity' to the Wraith there were no signs that there was any future danger to any of the local populations; so long as none of the natives drew attention to themselves by trying to tap into the Wraith telepathic network directly- and even if they knew how to do that, why would they have wanted to do it in the first place?-, I figured that it was easier to leave them alone."

"Just out of curiosity, why didn't the Wraith scientist just… feed on his test subjects and get rid of them that way?" McKay asked, looking uncertainly at the Phantom.

"Well, firstly, he didn't exactly make his plans with long-term containment in mind; given that he was operating without permission from the senior Wraith, he was the only person who even knew the experiments were going _on _in the first place, and he'd been relying on the cells and general fear of the Wraith to stop anyone trying anything, but he figured that couldn't lost long enough for him to fine-tune the experiments to accomplish his goal while eliminating the side-effects," the Phantom explained. "As for why he didn't just feed on them when things got ugly… well, Wraith can get gorged just like anyone else, and the guy had reason to believe that his fellow Wraith were coming close to finding out what he was up to; he wasn't sure he had enough time to feed on _everyone _there before they were able to break out and try to escape, so he figured it was easier to let them go and hope they either died or proved unable to pass on their 'gift' to subsequent generations."

Noting their slightly sceptical expressions, the Phantom shrugged. "Hey, I'm not exactly a Wraith psychologist; I'm just telling you what I've gathered from the information available at the base, I can't be certain _why _the bastard didn't just kill them when he knew it wasn't working out."

For a brief moment, there was simply silence as the rest of the people in the room processed the information they had just learned, before Teyla spoke at last.

"I… have never been able to sense the thoughts of the Wraith," she said, looking slightly uncertainly at the Phantom. "Are you certain that the scientist whose work you discovered is the reason for my peoples' gift? Could it not be something we… _evolved_, is the term I believe you use for such changes… over time to protect ourselves from them?"

"Possible, but unlikely; you'd need some kind of psychic ability to begin with for that to be the case, and all records I've discovered regarding Athos in the Atlantis databanks make it pretty clear that it was never populated by anything more than average humans while the Ancients were active," the Phantom said, shaking his head before he continued his explanations. "Anyway, assuming that you are descended in some way from the Wraith test subjects- which all the evidence I've gathered assures me is indeed the case-, my best guess is that, over the years, your people subconsciously repressed that ability to stop themselves from having to deal with some of the stuff they were picking up; if we can get past that- I've picked up a few meditation techniques over the years that might help you do the job-, we might be able to 'trick' the Wraith into thinking that we're going to blow up the city-"

"Oh, _now _I get it!" McKay said, a smile spreading across his face as he looked at the Phantom. "If we can trick the Wraith into thinking that we're about to detonate the ZedPMs-"

"The city has automatic safeguards to dampen the explosive potential of the ZPMs in the event of an overload, so the scenario you're proposing wouldn't work even in theory; in any case, after all the effort they've put into trying to take Atlantis in the first place, I'm not expecting the Wraith to back off because of something they _think _we're going to do," the Phantom interjected, looking at McKay with a slightly frustrated gaze that Sumner had to admit he sympathised with; it was almost frustrating that this man could _never _seem to do anything that Sumner wouldn't essentially approve of in the end. "The plan's a bit more complicated than that; after Teyla 'alerts' the Wraith hive-ships of our intentions by accessing the telepathic network, we wait for them to stop firing- given that they want access to Atlantis they're unlikely to want to continue doing anything that would help us destroy the city-, and then, as _Daedalus _departs, they beam a nuclear bomb directly above the city's shields and detonate it."

"And… then what?" Sumner asked, looking sceptically at the masked man. "We don't exactly have the power to sink the city to make it look authentic, and even if we could there's a chance it'd take too long to completely conceal the city from the Wraith…"

"Precisely why we're going to cloak the city instead," the Phantom clarified.

Elizabeth blinked.

"_Cloak _it?" she repeated, looking in confusion at the Phantom.

"Well, the principle's straightforward enough; after leaving the shield on just long enough to protect us from the hard radiation generated by the explosion, we switch the shield generator over to a stealth cloak generator- simply remove a cloak generator from a… gateship… and link it up to the shield; the procedure is fairly straightforward- and we can safely cloak the city to conceal it from all Wraith scanners," the Phantom explained. "All we need is good timing and a bit of luck, and we're sorted."

"Luck?" Caldwell repeated, looking with renewed intensity at the Phantom with that last comment. "Why is _that _a factor?"

"Well…" the Phantom said, once again appearing slightly uncomfortable as he looked at the colonels. "You see, by cloaking the city like that, we'd essentially be _replacing _the shield with the cloak, which means that if the Wraith _do _start firing on us while we're cloaked…"

"The city will be blown to pieces because it's utterly defenceless," Caldwell concluded.

"Pretty much, yeah," the Phantom confirmed, nodding slightly uncomfortably at the colonel. "It's a long shot, I know, but if you've got any better ideas I'd like to hear them."

After a brief exchange of glances with Caldwell, Sumner knew that he and his counterpart were on the same page; there wasn't any time to think of something else.

"All right," he said, glancing over at Caldwell. "We'll have all non-essential personnel transferred to the _Daedalus_ in the event that a quick escape's required if this plan doesn't work; McKay, you and Zelenka see what you can do about wiring a cloak generator up to the city's shield, while the… _Phantom_… does what he can to help Teyla tap into the network."

"Good plan," the Phantom said as he stood up, the rest of the people around the table following suit as though his actions had been a 'cue'. "Let's move."

* * *

"OK," John said as he sat opposite Teyla in her quarters, candles illuminated around them to better aid Teyla in entering the right mindset- they'd relocated to her quarters to attempt the meditation exercises he'd suggested; McKay and Zelenka were currently working on linking the city's shield generators to a cloaking generator from a 'gateship' while Elizabeth organised the evacuation of all but the most essential personnel to the _Daedalus_-, "with the Wraith so close to us in such large numbers at the moment, gaining access to the network shouldn't be difficult; the tricky bit is making sure that you get _in _without anyone else getting _out_."

"In… what sense do you mean… getting _out_?" Teyla repeated, looking at John in confusion.

"Look, the fine details aren't important; we can talk about the specifics of this ability of yours later," John said, waving a dismissive hand even as he admitted to himself that there probably wouldn't be a later even if this worked given his current reputation; he wasn't going to start kidding himself that Earth as a whole would be any more keen on hi continued presence in Atlantis than Sumner had been so far just because he helped them out during this mess. "All that _matters _is that you need to stay focused here; make sure the Wraith get the clear impression that we're willing to destroy Atlantis rather than let it fall into their hands, but don't 'stick around' any longer than that."

"I… will try," Teyla said, nodding uncertainly as she faced the man before her. "But… what you ask of me… it is beyond anything I have ever done…"

John could only nod at her.

"I know," he said, looking sympathetically at her. "Believe me, if there had been a better way to bring up the matter of your heritage and lead you into this, I would have done so, but we can't afford to worry about that right now; you _really _need to focus if this is going to work."

Nodding in understanding, Teyla sat back once again and closed her eyes, John taking up position opposite her.

"OK," he said, looking calmly at her. "To begin, stop paying attention to the world around you. For the moment, there is nothing else around us but you and my voice. Focus on that feeling you get when you are aware of the Wraith… return to the darkness within… conceal yourself in that darkness…"

For a moment he simply sat in silence, waiting for Teyla to respond, until she finally spoke.

"I… I am on a hive-ship…" she whispered, her voice low as though concerned that someone would hear her. "I am among Wraith… they are all around me…"

"You're not _really _there, Teyla; this is just your mind's way of coping with stimulus it was never intended to receive," John said, trying to keep his voice low to avoid snapping her out of it before they were finished. "You're accessing the Wraith telepathic network; all youneed to do right now is send them what we want them to hear."

"Of course…" Teyla said, her voice trailing off as she raised her head slightly, the better to focus her attention on what she was doing. For a moment there was silence, Teyla's eyes twitching slightly as though she was dreaming as John stared anxiously at her, and then Teyla's eyes opened sharply, smiling briefly at John as she did so.

"It is done," she said simply. "I made contact with the Wraith, and the thought of destroying Atlantis was first in my mind; if the screams of defiance I sensed are anything to go by, they are evidently not eager to lose the city…"

Her voice trailed off as John tilted his head slightly to one side, apparently listening for something, subsequently smiling as he looked back at her.

"The firing's stopped," he said by way of explanation, indicating the ceiling above them; even when listening intently, he could no longer hear the sound of the Wraith weapons pounding against the shield. "Your message must have gotten through; all we need to do now is wait, and-"

"_Doctor Beckett to… Phantom_?" Beckett's Scottish voice suddenly said over the radio, cutting him off mid-sentence. "_We have a problem; Lieutenant Ford's regained consciousness and is on the move even as we speak_."

John blinked.

"_WHAT_?" he yelled, staring incredulously at the radio, his conversation with Teyla forgotten in light of this newest complicated. "But he's-"

"'_Doped up to the eyeballs on Wraith enzyme', I believe was the term you used, correct_?" Beckett asked, his tone displaying his anxiety as he spoke. "_He's taken all the enzyme I've harvested from the Wraith bodies and seems to be heading for the gateroom; I've called Sumner, and I've even tried to speak to the lieutenant, but he's nowhere _near _interested in listening to me in his current state, and with the military down to the basics to prepare for evacuation we just don't have the manpower_-"

"Call them back," John said, standing up and pulling out his gun, shooting an apologetic glance at Teyla for leaving her like this before he headed for the door. "I'm the only person available who knows what Ford's really capable of in his current state; I'll take it from here."

With that he turned around and hurried out of Teyla's room, already calculating the most likely route from the infirmary to the gateroom that Ford would take, trying not to think about the irony that he was about to go up against someone on Wraith enzyme after spending so long keeping a sample as a 'secret weapon'…

For a moment his hand strayed to the pocket where he kept his phial of enzyme once again, but he drew his hand away almost instantly; in this situation what was required was a clear head to out-think Ford's current inclination to rely on brute force to solve his problems, and the enzyme- in any dosage- would compromise that ability significantly…

John tried not to think about the issue that use of the enzyme could leave him in a state here he'd be inclined to do something he'd regret when he had a clear head; he'd never been entirely certain what effect the enzyme had on his judgement after using it- given that he'd only ever used it in a fight his decision had generally been limited to nothing more complicated than who to attack first, particularly since he always left his fights fairly quickly once he'd finished off his foes-, and he wasn't about to risk finding out what he might do _this_ way.

If he encountered Elizabeth while on the enzyme and did something he'd regret later…

Turning around a corner, John's eyes instantly fell on Ford as the lieutenant ran towards the door at the other end, his gun in his hand as he stared intently at the other end of the corridor, and thoughts of Elizabeth had to be pushed aside; he had more immediate matters to deal with right now than the question of what he _might _do.

"_Lieutenant Ford_!" John yelled, aiming his gun at the young man before him, his finger already tightening on the trigger.

As the lieutenant spun back around, John couldn't restrain the slight wince at the sight of Ford's face; the memories conjured up by the sight were areas he _really _didn't want to get into right now…

"What are _you _doing here?" Ford asked, glaring angrily at the masked man before him.

"I'm here to take you back to the infirmary; what else?" John responded, staring intently at the other man; talking calmly to someone in this state might not work, but he might manage to convince the other man to make a mistake that would leave him vulnerable if he pushed him too hard. "You're not well-"

"Oh, you'd like that, wouldn't you?" Ford spat, glaring at John in contempt. "You'd like to remain the city's _hero_, swooping in to save the day all the time and leaving us all looking like pathetic _idiots_; you just can't _take _the fact that there's someone _else _out here now who can do _just _as much damage to the Wraith as you can-"

"You're barely thinking rationally right now, lieutenant; that enzyme _seriously _disrupts your brain chemistry!" John interjected, glaring in frustration at the man before him. "You _might _be able to outlast a Wraith in a fight in your current state, but you're also barely capable of thinking of any strategy more elaborate than 'hit it until it's dead'; you _need _to come back-"

"What, to a city where people _listen _to a renegade element like _you_?" Ford countered, glaring at the man before him. "At least I'll have _training _when I go out there; where did _you_-?"

Before anything further could be said- not that John thought it likely either of them would make any impact on the other in this confrontation; Ford's condition made rational debate virtually impossible-, the city suddenly shuddered as though something had struck it- most likely the aftermath of the nuclear bomb they were using to trick the Wraith, John noted with a brief part of his mind; he vaguely recalled hearing a message from Elizabeth earlier, but since he'd turned off his radio while looking for Ford it hadn't been that clear and they were too deep inside the city-, sending John stumbling off his feet and giving Ford a chance to turn around and enter the teleporter just behind him before John could regain his balance.

Cursing at his ill luck, John hurried into the teleporter as quickly as he could, selected the teleporter Ford had just travelled to- recently-used teleporters tended to register a slight 'warning' signal if they'd been used anytime in the last few seconds; John speculated that the Ancients had used it to prevent accidents caused by someone trying to go to a booth when someone was getting out of it-, subsequently departing just in time to see Ford hurrying down another corridor that, if memory served, led towards the 'gateship' bay.

_Damnit_! John cursed inwardly as he hurried after the lieutenant down the currently-empty corridor, praying that he'd reach the bay in time even as he knew he wouldn't; with that enzyme currently in his system, Ford was capable of outpacing him by a not-inconsiderable amount even without his head-start…

Hurrying into the gateship bay, John was just in time to see Ford enter one of the ships- he might not be able to pilot it long distances himself, but the gateship's automatic autopilot when in Atlantis would at least help him get through the Stargate without being stopped-, John diving through the rear hatch- he vaguely registered Zelenka's unconscious body lying alongside the ship, but he didn't have time to worry about that right now- after Ford just as the lieutenant had set the ship into motion. Even as the gateship rose up and began to move into position to descend, John had already drawn his gun and fired it at the lieutenant, only for the stun-blast to do little more than annoy the other man as he grabbed John by the cloak.

"We were better off _without _you here undermining everything!" Ford yelled, John vaguely registering the gateship's descent into the main control room- he'd learned over the years- as his deranged opponent glared at him. "If they _want _a 'vigilante' taking action here, maybe they'll let me go when I get _rid _of you!"

John vaguely had time to wonder what train of thought had led Ford to that conclusion- maybe he thought that the senior staff hadn't found him because they were _deliberately _trying not to and thought that they'd leave him alone if he proved himself 'superior' to the Phantom?-, but then he felt himself start to fly backwards and instantly reached for another pocket…

* * *

Looking back, Elizabeth wasn't certain what had startled her more; the moment when the Stargate activated (Becaue she'd had absolutely no idea what had caused it) or the moment when the gateship descended from the ceiling and a black-clad form that could only be John was hurled out of it (Becaue she definitely hadn't expected _that_ to ever happen; she'd grown so used to the idea of John as the seemingly-indestructible Phantom that the idea of something in Atlantis being able to throw him like that seemed almost impossible), the body striking the steps hard even as the gateship rotated to face the Stargate.

For a moment Elizabeth was tempted to hurl caution to the wind and hurry down the stairs to see how John was, but then he leapt to his feet and Elizabeth caught a brief glimpse of something green under his cloak- evidently an Ancient shield device- before he was hurrying up to the control room, urgently glaring at McKay.

"Ford's in there; shut down the wormhole!" he yelled at the Canadian scientist.

"I _can't_; the gateship's in control!" McKay countered., looking in frustration at the Phantom.

"Can they detect the wormhole?" Elizabeth asked, looking over at McKay.

"The cloak _might _be able to shield it from them, but that's not the only issue," McKay said, his grim expression making it clear that he didn't have good news for her. "If he gets away…"

Elizabeth understood McKay's point all too well; if Ford got away now, then all their efforts to save Atlantis could be undone.

"Lieutenant Ford," Sumner said, activating his radio as he glared at the gateship. "I am ordering you to _stand down_; this is a _direct order_!"

For a brief moment, the gateship simply hovered in front of the Stargate, as though Ford was contemplating the orders he'd just received, but then the gateship moved through the Stargate, the wormhole shutting down as soon as it vanished.

"_Damnit_…" John muttered where he stood beside her, staring grimly at the now-deactivated Stargate. "_That _could have gone a hell of a lot better…"

"The question is, did they detect it?" Sumner asked, jerking his head up slightly to indicate where the Wraith ships still hovered above Atlantis.

For a moment, the sparsely-populated control room stood in silence, everyone inside it holding their breath as they waited for what might happen next, until a radio call from the _Daedalus _finally broke the silence.

"_This is _Daedalus," Caldwell's voice said over the radio. "_Our sensors indicate_

"I can confirm that; they're headed for hyperspace," McKay added, glancing briefly at his laptop before looking up at the others. "I'm gonna keep the cloak up for a while just to be sure, but… I think they bought it."

Nodding in acknowledgement at McKay, Elizabeth walked over to where John and Sumner stood on the balcony, staring at the Stargate where Ford had vanished through mere moments ago.

"We can find the gate address in the log…" she said, already knowing as she said it that her suggestion wouldn't work.

"It doesn't matter where he goes," John said simply. "The second he gets to wherever he's going, he's gonna ditch the Jumper, turn around, and dial another address that we _can't _trace; he's gone."

"Yep; he got away," Sumner confirmed, nodding grimly before he turned to look at the Phantom. "And so did you."

Of all the things Elizabeth had been expecting to hear Sumner say to the Phantom, that hadn't been anywhere near the top of the list.

"Pardon?" John said, looking with at-least-slight incredulity- the mask made it hard to be certain- at the man before him.

"Due to lack of manpower in this area, you got away from the control room in the confusion caused by Ford's departure," Sumner clarified, briefly indicating the rest of the people in the gateroom; aside from those in the control room itself, the area was practically deserted. "As of yet, my teams have been unable to locate you in the city, although I will naturally order search parties to resume their efforts to track you down once normal operations have resumed after the debriefing on Earth…"

Noting the Phantom's evident confusion, Sumner sighed. "Look, I'm not saying that I like you any more than I did before this whole mess- you're still a potential hazard who could prove dangerous at some point down the line if he continues to insist on doing his own thing-, but, after what you've just saved us from…"

The colonel shrugged. "Let's just say I'm… willing to allow for the fact that you're of more use to us at present as a free agent rather than confined to a cell somewhere…"

"So long as I continue to coordinate with you when the need arises and we face another crisis of this scale, correct?" John replied, the slight smile under his mask now evident to all as he nodded at Sumner. "You know… you're not that bad."

"Go," Sumner said briefly in response, indicating the nearest door, only the slight smile on his lips any indication that he had even heard the Phantom's response in the first place.

With one last nod, John turned around, jumped off the balcony, landed in a roll on the lower level that culminated in him being on his feet and moving in a matter of seconds, subsequently hurrying through the door before him and back into the depths of the city that he knew better than anyone.

Even with the loss of Lieutenant Ford- to say nothing of the men they'd lost during the Wraiths' initial assault on the city-, Elizabeth couldn't help but smile.

They'd saved Atlantis, destroyed at least five Wraith hive-ships, would soon be heading back to Earth, _and _Sumner even seemed to be more accepting of John's presence…

And why was that last one so important to her?

More importantly, how come she'd only just realised that she'd forgotten to consider the possibility of seeing Simon again?

* * *

AN: In case anyone's wondering why John didn't just suggest that he go and pick up some extra ZPMs from his offworld storage facility to help with the hive-ships, the reason is that he's fully aware that using those ZPMs would only be a temporary measure that would do nothing but buy time- particularly given the limited number of drones currently stored in Atlantis, thus limiting their opportunities to strike back-, so he doesn't see any point in mentioning it as it wouldn't do them any real good (Coupled with the fact that he's doubtful Sumner would allow him out of the city long enough to pick them up).


	37. Back to Earth

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Thanks are due to Manic Penguin, whose story 'Connections' inspired some of the plot elements I'll be using in the next few chapters and subsequently gave me permission to use whatever I wanted for my own work (Although I'm naturally putting my own spin on things)

The Phantom of Atlantis

A few days after the conclusion of the siege, the last remnants of the Wraiths' temporary presence in Atlantis cleared away and any damage caused by their attacks already being repaired, Elizabeth sat in her office going over the files and messages- many preferring to 're-do' the more grim messages they had sent to their families prior to the siege- her staff had prepared in response to the news of the upcoming trip back to Earth.

Although the _Daedalus _was already on its way back to Earth- a round trip of almost a month without a ZPM available to enhance their power-, the new SGC commander General Landry- along with a new group referred to in the paperwork Elizabeth had received as the 'International Oversight Agency'; apparently General Landry had been - had requested the presence of Atlantis's senior staff to go over some details about resource and personnel allocation in light of their renewed ability to contact Earth… which, Elizabeth was already certain, would result in her facing several questions about her command decisions that she was _not _looking forward to, starting with her actions regarding allowing the Athosians access to the city and working their way up from there.

In spite of that particular complication, however, everything was going fairly well in Atlantis at the moment; even the latest revelation regarding Teyla's Wraith DNA had gone down fairly well once it had become known to the general population. A few expedition members had been slightly uncomfortable about the implications of that particular genetic quirk at first, but in general everyone had accepted the view that Teyla was no more a Wraith than those with the Ancient gene were Ancients and left it at that.

It was probably going to cause some problems with the 'IOA', of course, but after Teyla's genes had helped them save the city from the Wraith, and with Teal'c and Jonas Quinn to serve as an example of a precedent of an alien serving in a prominent role on an SG team- to say nothing of their long-term alliance with the Jaffa-, she was fairly certain she could convince them to leave the Athosians where they were…

Quite frankly, even with most of the expedition focused on nothing more than sending messages to their loved ones- or, in the case of those coming with her and the senior staff back to Earth, making arrangements to visit their loved ones; organising files and mission reports were the sole responsibility of the department heads at this time-, the issue of the Phantom remained the biggest problem facing Elizabeth; she had no idea _how _she was going to deal with the complications that would arise regarding the SGC's opinion of his presence in Atlantis. Admittedly, General O'Neill seemed to be on his side based on his comments when they'd first regained contact with Earth, and the aid he'd provided for them during the siege would go a long way towards proving that he _could _cooperate with them if the situation called for it, but she somehow doubted that the rest of the SGC would see things that way…

On the bright side, the recent collaboration with the Phantom seemed to have gone some way towards improving his relations with the expedition's military division, particularly in regard to Sumner's opinion of him. Elizabeth acknowledged that the colonel was never going to be John's biggest fan, but he at least seemed to be prepared to try and give the other man more leeway than he had in the past; the fact that he'd allowed John to escape when he could have easily at least attempted to capture him said a lot for his new willingness to consider tolerating the Phantom's presence in the city.

In the end, she supposed that all she'd have to do was keep her fingers crossed and hope for the best; John had helped them out so far when there'd been no reason for him to do so, given their status as the 'aggressors' (They may not have taken any explicit action against him, but they _had _'invaded' his home and set themselves up there without asking him), as well as avoiding actually doing any damage to them in retaliation, but whether that would count for anything in the eyes of some of the bureaucrats back on Earth was something Elizabeth just didn't know.

Hell, when you got down to it, it hadn't been long ago that _she'd _been one of those bureaucrats, hiding behind official forms and regulations while making decisions- she'd tried to _negotiate _witha group of_ Goa'uld_, for God's sake-; she knew all too well how easy it could be to hide behind what seemed good on paper to avoid having to make the more 'risky' decisions, and trusting someone they know as little about as they knew about the Phantom was _definitely _a risky decision. General O'Neill might have told Sumner to ask the Phantom for assistance during the Siege, but aid during a crisis was one thing; expecting the SGC overseers back on Earth to trust the Phantom on a long-term basis might be more difficult…

"Doctor Weir?" Sumner said, prompting her to glance up from the paperwork to see her military commander standing at her door. "The science teams have almost finished sorting out the artefacts for the archaeology departments back on Earth, and McKay tells me that the science teams have organised everything they think Earth would be interested in; we're ready to go whenever you are."

"And I assume that McKay's got everything he claims he needs to get the SGC convinced that he requires more than the already-large scientific team he's been provided with already, correct?" Elizabeth asked, smiling slightly as she stood up from behind the desk. "For a man who always goes on about how he doesn't need the staff he already has, he _does _seem to want a lot of help…"

"Probably an ego thing," Doctor Beckett added as he walked into the office, smiling slightly over at the two of them; evidently he'd finally managed to guarantee that those left in charge of his department during his time on Earth would manage fine in his absence. "You know, like some people get big cars to… compensate… for other areas, Rodney likes a big department to… well, just to show off, really."

"Right…" Elizabeth said, nodding uncertainly at the Scottish doctor- the implications of his theory weren't something she was entirely comfortable with; the idea of Rodney McKay having sex wasn't something she was sure she'd _ever _be comfortable thinking about- before she looked back at Sumner. "Well, we'd better be off; they're waiting for us back… at the SGC."

Neither of the men before her bothered to ask what she meant by that last comment; Sumner may have made it clear that he primarily saw Atlantis as another assignment rather than anything else, but even he had evidently come to see Atlantis as more of a home than a simple place of business.

Earth might be the place where they had been born, but Atlantis- for all that they had only been here for a few months- had already become their home (Even if Elizabeth at least was starting to consider herself more of a tenant; John might be officially a 'renegade' in this city from Earth's perspective, but she couldn't help but regard him as the real owner who just let them live there).

Actually, looking over the personnel files before her as her visitors returned to their tasks- Carson shooting her an apologetic smile-, so far Elizabeth had only discovered one request for transfer back to Earth, and given that the request came from Doctor Kavanagh- the man had been frustrating even before she'd rejected his initial suggestion to raise the shield during that incident when the gateship got stuck half-way through the Stargate, and had just become ever more insufferable afterwards- nobody was that concerned about his departure (Although Elizabeth had found herself wondering why he'd become rather more jumpy than annoying ever since they'd sent messages back to the SGC; every time she entered a room where he was working, Kavanagh always seemed to go out of his way to get out of it as quickly as possible…).

Shaking thoughts of that frustrating doctor aside, Elizabeth turned her attention back to the matter before her; they were going back to Earth tomorrow, and she _still _hadn't finished sorting out who'd be coming back with them and who would remain in charge of the city in their absence. Teyla would have been her first choice as her 'stand-in', but Sumner- no matter how much he respected Teyla as a teammate or with his recent collaboration with the Phantom- still felt uncomfortable entrusting Atlantis to someone who hadn't come from Earth, which meant that Elizabeth had to make a choice between Zelenka, Doctor Viro- Carson's selected 'second'-, or just attempting a compromise by the previously-mentioned men and Teyla in charge all together.

In the end, that one would probably work out more efficiently; at least that way she wouldn't be left worrying about how one of her staff would cope with a workload that even _she _had trouble with, given that they'd all be focusing simply on taking more direct responsibility for their own departments (Especially since all 'gate activity would be suspended until their return from Earth to focus on reconstruction of Atlantis)…

Sighing briefly at herself, Elizabeth returned her attention to the more immediate matter of tying up the last loose ends left to her; if she didn't sort out specifically who was responsible for what soon she'd reach the point where she was too tired to properly concentrate.

She was just grateful that she didn't have far to go to talk to her family while also trying to accommodate talking to the political support in Washington, given that Simon and her mother were both in that city; Carson going away to Scotland for a few days to visit his family was already more of a separation than she was entirely comfortable with (Although she freely acknowledged that it was mainly increased familiarity after spending so long with the same group of people that was responsible for that issue), and she'd prefer to remain as 'on-sight' as possible when discussing something as important as Atlantis's future.

After spending so long struggling just to survive out in the Pegasus Galaxy, it would be nice to be able to guarantee for her staff that they would no longer have to worry about struggling for some of the necessities like food or clothing in order to operate on a daily basis like they'd been trying to do ever since they used up their initial supplies (Which wasn't to say trade wouldn't continue; some of the clothing they'd acquired in their more recent deals was actually rather comfortable…).

Finally, after filling in so many forms that she felt like her wrist was going to come off from exhaustion, Elizabeth signed her name on the last dotted line of the last form before her- she'd had to go back over a couple to make sure she hadn't missed something from fatigue, but in general she was comfortable with how things had turned out- and stood up to head for her room.

Right now, after the stress and challenges of the last few weeks- even with John's help they'd lost far too many people- , she just wanted to curl up in her bed and get away from the stress of running a city as elaborate as Atlantis for a while.

If she could just get a few hours' uninterrupted sleep, away from Sumner's military-fixated mindset and McKay's occasional panic/frustration attack about everything from the 'incompetence' of his staff to his own health, she was sure that she'd feel _far _better in the morning…

* * *

As she stood in front of the Stargate the following morning, however, despite being well-rested and secure in the knowledge that she'd dealt with everything she could deal with in order to make it as easy as possible for her 'replacements' to cope with whatever paperwork they might have to tackle over the next month, Elizabeth knew that she'd been kidding herself.

No matter how hard she tried, she couldn't stop her thoughts from coming back to the central issue she'd be facing when she got back to Earth; the presence of the Phantom at the SGC. The issue of their reaction to the Wraith was a definite danger, but there was no way anyone could blame _her _for their 'waking up'- even Sumner would have nothing to worry about, given that the Wraith had only 'activated' because of Lieutenant Ford's actions and the lieutenant certainly wasn't around to deal with the consequences of that decision-, and her dealings with the Genii only turned out badly after _they _betrayed Sumner's team, which meant that the presence of the Phantom in the city was the only issue she would _really _have trouble dealing with.

The Wraith might be dangerous, but in the end the IOA could be relatively certain how they were going to act, especially after learning about their interest in Earth; Elizabeth could already predict multiple 'lectures' about the dangers of an independent renegade element like the Phantom operating in the city…

Pushing those thoughts aside once again- she could worry about how she'd deal with those questions when she was actually in position to answer them-, Elizabeth took a deep breath and turned around to look at the group of expedition members who had gathered together for their trip back to Earth.

"It's been a long year for all of us," she said at last, her mind briefly flashing back to all the faces who hadn't lived to see this day (She knew that it was actually a couple of months short of a year, but now was hardly the time to get bogged down in details like that). "We've seen and accomplished things that none of us would have believed possible even after learning about the Stargate program, confronted an enemy more ruthless than even the Goa'uld, and found ourselves learning that even the place we thought would be our exclusive home has a few… surprises… in it for us," (She avoided specifically naming the Phantom even if she knew that everyone would know who she was talking about; that particular issue was one area that she wanted to keep out of the 'public eye' as much as possible), "but, in the end, we've not only managed to survive, but we succeeded in fighting off a foe so powerful that they all but totally defeated the Ancients. It's been an incredible experience, and I'm proud to have shared it with all of you…"

She swallowed for a moment, briefly wishing that she had the freedom to say what she really wanted to say- that she'd come to respect and admire so many of them as friends-, but knowledge of Sumner's preference for emotional detachment, combined with the risk if she said something that might even _hint _at her contact with John, kept her from saying anything.

"…and now," she continued, her composure regained once more, "it's time to return to Earth so that others know what we have discovered here, and give the rest of humanity a chance to benefit from what we've learned. We've all come a long way since we first arrived here; it's time to let the people we left behind know what we've accomplished."

Glancing up at the balcony where Teyla and the rest of the control room staff were watching her- everyone else was presently too busy with the repair work and checking out some of the newly-activating systems that were becoming available with the new ZPM to be here-, Elizabeth gave the Athosian woman a brief smile of approval, before she turned back around to walk through the Stargate, ready to return to the world that now was only her home due to the location of her birth…

* * *

As Elizabeth led the small group back through the Stargate, she was unaware of the darkly-clad figure watching her from his usual position on the other side of a small hatch near the ceiling of the room, a slight smile on his face under his mask as he watched her.

He'd done it.

Even when faced with a Wraith fleet on a scale this galaxy hadn't seen since the Ancients, Elizabeth had lived to make it back to Earth…

John tried to restrain the brief pain he felt in his heart at the thought of what was coming next, but he couldn't help it.

She hadn't just made it back to Earth (Although that was the most obvious part of the trip she'd just taken through the Stargate); she'd made it back to _Simon_.

Even if the Elizabeth he'd met all those years ago had only briefly mentioned the man she was planning to marry before she was given command of the Atlantis expedition during her talk with him, the possibility that the Elizabeth he would meet when the time came for the expedition to arrive would go back to Simon in the end- to say nothing of his _own_ feelings about that particular issue- had always been one of the many little personal issues he'd struggled to overcome during his time alone (Along with other matters such as his reaction when he found himself dreaming about Elizabeth… _that_ way… in the first place and working his way up from there).

If she couldn't persuade Simon to come back to Atlantis with her now that they had the ability to regularly return to Earth…

Would she stay with _him_?

Atlantis might be the most incredible experience of a person's life, but it didn't exactly make it easy to create a normal life for yourself; if Elizabeth had a chance at happiness…

If she had a chance with Simon, she deserved to take it.

_She deserves better than a life with a monster_…

Shaking that thought aside- the last thing he wanted was to start getting negative about his own sense of worth when Atlantis was due to get a serious personnel upgrade in a matter of weeks; no matter what Sumner had done for him at the end of the siege there was no guarantee his superiors would be as tolerant, which meant he'd probably have even _more _soldiers to avoid-, John turned around and began to head towards one of his old storerooms.

If he was going to figure out what to do with himself if the worst came to the worst and Elizabeth _did _leave Atlantis (Thus costing him his only _real _ally on the senior staff; even without Sumner's evident discomfort at anything related to him, McKay still clearly wasn't entirely certain about him and Teyla and Beckett's authority over the kind of situations he might create by his presence was limited), he might as well do it somewhere comfortable…

* * *

AN 2: Well, that's the first part of this series over; the next part, "Mystery of the Phantom", will be up as soon as possible, I can assure you (I just can't give you a specific time-frame at this point)


End file.
